This README file was generated on 2024-03-21 by Liming Zhang.

GENERAL INFORMATION

1. Title of Dataset: A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes

2. Author Information:

   A. Principal Investigator Contact Information

   Name: Gong Cheng

   Institution: Tsinghua University

   Address: Beijing, China

   Email: gongcheng@tsinghua.edu.cn

   B. Co-investigator Contact Information

   Name: Yibin Zhu

   Institution: Tsinghua University

   Address: Beijing, China

   Email: zhuyibin@tsinghua.edu.cn

3. Date of data collection (single date, range, approximate date): 2021-2024
4. Geographic location of data collection: Yunnan, China
5. Information about funding sources that supported the collection of the data: This study was supported by grants from the National Key Research and Development Plan of China (2021YFC2300200, 2022YFC2303200, 2021YFC2302405, 2023YFA1801003, 2021YFC2300900, and 2022YFC2303400), the National Natural Science Foundation of China (32188101, 82102389), the Shenzhen San-Ming Project for Prevention and Research on Vector-borne Diseases (SZSM202211023), the Young Elite Scientists Sponsorship Program (2021QNRC001) , the Science and Technology Project of Southwest United Graduate School of Yunnan (202302AO370010), Basic Research Projects of Yunnan Province (202201AS070062). The New Cornerstone Science Foundation through the New Cornerstone Investigator Program, and the Xplorer Prize from Tencent Foundation.
6. The DOI of this Dataset: https://doi.org/10.5061/dryad.59zw3r2g6

DATA & FILE OVERVIEW

1. File list:

   (A) README.md

   (B) Alignment_of_Rosenbergiella_sp._YN46_and_other_related_bacteria.fas

   (C) Rosenbergiella_sp._YN46_16s_1414bp.fa

   (D) Phylogenetic_tree_of_Rosenbergiella_sp._YN46_and_other_related_bacteria.mtsx

   (E) Selected_protein_sequences_of_Rosenbergiella_sp._YN46.fa

   (F) Phylogenetic_tree_of_Rosenbergiella_sp._YN46_and_other_related_bacteria.png

   (G) Rosenbergiella_sp._YN46_draft_genome.fasta

   (H) Wenshan.zip

   (I) Lincang.zip

   (J) Puer1.zip

   (K) Puer2.zip

   (L) Xishuangbanna1.zip

   (M) Xishuangbanna2.zip

DATA-SPECIFIC INFORMATION

1. For README.md:

   Description: This file.

2. For Alignment_of_Rosenbergiella_sp._YN46_and_other_related_bacteria.fas:

   Description: Alignment of Rosenbergiella sp. YN46 and with other related bacteria

   Number of bacteria: 24

3. For Rosenbergiella_sp._YN46_16s_1414bp.fa:

   Description: Sequence of Rosenbergiella sp. YN46 16S rRNA

   Number of base pair: 1414

4. For Phylogenetic_tree_of_Rosenbergiella_sp._YN46_and_other_related_bacteria.mtsx:

   Description: Raw data for Phylogenetic tree of Rosenbergiella sp. YN46 and other related bacteria

   Software: MEGA11

   Statistical Method: Neighbor-joining

   Test of Phylogeny: Bootstrap method

   No. of Bootstrap Replications: 1000

   Substitutions Type: Nucleotide based on 16S rRNA

   Model/Method: Maximum Composite Likelihood

   Substitutions to Include: Transitions + Transversions

   Gaps/Missing Data Treatment: Pairwise deletion

5. For Selected_protein_sequences_of_Rosenbergiella_sp._YN46.fa:

   Description: Sequences of Rosenbergiella sp. YN46 proteins identified by mass spectrometry in culture supernatant

   Method: Individual colonies of Rosenbergiella_YN46 were inoculated in BHI broth and cultured overnight at 30 °C. Following incubation, the bacteria were separated through centrifugation and filtration using a 0.22 µm filter (SLGP033RB, Millipore). The protein fraction of the bacterial supernatant was concentrated using an Ultra15 centrifugal filter concentrator (UFC900396, Amicon). Subsequently, SDS‒PAGE was conducted, with fresh BHI broth employed as a negative control. The entire gel lane was then excised and subjected to analysis by liquid chromatography‒mass spectrometry (LC‒MS) at the Protein Chemistry Technology Core, Tsinghua University. The MS readouts were cross-referenced against the protein sequence database of Rosenbergiella_YN46. The upper retentate of fresh BHI broth that was filtered through a 3 kDa centrifugal filter served as a negative control. The Rosenbergiella_YN46-derived proteins were identified after the protein components in the negative BHI control were excluded. With the subsequent investigation focusing on the top ten most abundant proteins containing >20 single peptides.

6. For Phylogenetic_tree_of_Rosenbergiella_sp._YN46_and_other_related_bacteria.png:

   Description: Figure for Phylogenetic tree of Rosenbergiella sp. YN46 and other related bacteria

7. For Rosenbergiella_sp._YN46_draft_genome.fasta:

   Description: Draft genome of Rosenbergiella sp. YN46

   Method: The genome of Rosenbergiella_YN46 was assembled as follows: sequencing libraries for Rosenbergiella_YN46 were prepared using the MGIEasy Universal DNA Library Prep Kit, and these libraries were subsequently sequenced on the DNBSEQ T series platform, producing 150-base pair paired-end read data. To prepare the data for assembly, read adapters and low-quality reads were eliminated using fastp. The genome was assembled using SPAdes (version 3.15.3) with default settings. Following the assembly, proteins within the bacterial genome were predicted and annotated using Prokka (version 1.14.6) and eggNOG database (version 5.0), employing default settings for the annotation process.

8. for Wenshan.zip, Lincang.zip, Puer1.zip, Puer2.zip, Xishuangbanna1.zip, Xishuangbanna2.zip:

   Description: Sequencing data of the midgut isolated from Aedes albopictus caughted from Wenshan, Lincang, Puer, Xishuangbanna

   Method: The RNA extraction process involved the midguts of A. albopictus from four distinct areas, and TRIzol reagent was used (15596026, Invitrogen). Subsequently, sequencing libraries were established through the use of the MGIEasy RNA Library Prep Kit V3.0. The RNA was fragmented, reverse transcribed, and converted into double-stranded cDNA. The resulting cDNA was subsequently subjected to dual indexing, amplification, and circularization to produce DNA nanoballs (DNBs), which formed a library. These libraries were subsequently subjected to sequencing on the DNBSEQ T series platform (MGI, Shenzhen, China), yielding metatranscriptomic data in the form of 150-base pair paired-end reads. For each individual sample, reads stemming from ribosomal RNA (rRNA) were eliminated using URMAP (version 1.0.1480) . Following this step, read adapters and low-quality reads were removed using fastp (version 0.20.1). Reads identified as duplicates and those displaying low complexity were further eliminated from the dataset using SOAPnuke (version 2.1.5) and PRINSEQ++ (version 1.2), respectively. Subsequently, the filtered reads were mapped against the SILVA rRNA database (Release 138.1) utilizing sortmeRNA (version 4.3.4), with the aim of further excluding any remaining rRNA sequences from the dataset.

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
2. Links to publications that cite or use the data: Liming Zhang, et al. (2024), A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes.
3. Recommended citation for this dataset: Zhang, Liming; Cheng, Gong; Zhu, Yibin (Forthcoming 2024). A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes [Dataset]. Dryad. https://doi.org/10.5061/dryad.59zw3r2g6

4. Links to other publicly accessible locations of the data:

   Rosenbergiella sp. YN46 16S rRNA:

   1. China National GeneBank DataBase, https://db.cngb.org/cnsa/; project accession: N_001485395.
   2. NCBI GenBank, https://www.ncbi.nlm.nih.gov/genbank/; project accession: PP213046.

   Rosenbergiella sp. YN46 draft genome:

   1. China National GeneBank DataBase, https://db.cngb.org/cnsa/; project accession: CNP0005149.
   2. NCBI GenBank, https://www.ncbi.nlm.nih.gov/genbank/; project accession: JAZHEE000000000.

   Metatranscriptomics of the midguts of Aedes albopictus caught from Xishuangbanna, Wenshan, Puer, and Lincang:

   China National GeneBank DataBase, https://db.cngb.org/cnsa/; project accession: CNP0005140.

   Selected protein sequences of Rosenbergiella sp. YN46:

   1. China National GeneBank DataBase, https://db.cngb.org/cnsa/; project accession: N_001485729, N_001485733, N_001485731, N_001485727, N_001485730, N_001485734, N_001485732, N_001485726, N_001485735, N_001485728.
   2. NCBI GenBank, https://www.ncbi.nlm.nih.gov/genbank/; project accession: PP296634, PP296635, PP296636, PP296637, PP296638, PP296639, PP296640, PP296641, PP296642, PP296643.