Dataset Information

Proteomic sequencing of Saccharomyces Cerevisiae CEN.pk 2-1D for HCAKing system

ABSTRACT: The HACKing system can rapidly and multiplexed integrate genes from a metabolic pathway into the target sites of chromosomes, which rationally formed a synthetic bicistron. This sequencing provides available target sites with different protein expressing levels.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: JIE MENG

LAB HEAD: Shuobo Shi

PROVIDER: PXD043249 | Pride | 2023-07-07

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	CEN_1_Slot1-30_1_6412.d.zip	Other
	CEN_1_combined.zip	Other
	CEN_2_Slot1-31_1_6413.d.zip	Other
	CEN_2_combined.zip	Other
	CEN_3_Slot1-32_1_6414.d.zip	Other

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Project description:BACKGROUND:More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such "molecular operational taxonomic units" (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries. RESULTS:We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered >?650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; >?99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.). CONCLUSIONS:We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.

Dataset Information

Proteomic sequencing of Saccharomyces Cerevisiae CEN.pk 2-1D for HCAKing system

Dataset's files

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