Taxonomic analysis of avocado (Persea americana) bark and rhizosphere soil samples

Data analysis for the article:

Bark from Avocado Trees of Different Geographic Locations have Consistent Microbial Communities

Eneas Aguirre-von-Wobeser¹*, Alexandro Alonso-Sánchez², Alfonso Méndez-Bravo³, Luis Alberto Villanueva Espino³, Frédérique Reverchon²

¹CONACYT – Centro de Investigación y Desarrollo en Agrobiotecnología Alimentaria, Centro de Investigación y Desarrollo, A.C., Blvd. Sta. Catarina s/n, Col. Santiago Tlapacoya, 42110, San Agustín Tlaxiaca, Hidalgo, Mexico

²Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, Col. El Haya, 91070, Xalapa, Veracruz, Mexico

³CONACYT – Escuela Nacional de Estudios Superiores, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Col. Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico

*Correspondance: E. Aguirre-von-Wobeser eneas.aguirre@ciad.mx

Instuctions to view complete taxonomic composition of avocado bark and rhizospheric soil samples:

1. Go to the section Kaiju taxonomic analysis interactive plots.
2. Scroll down to the desired sample.
3. Click on "View Report in Separate Window"
4. Click the link on the upper right, ending with the word "Krona"
5. In the plot, click on the different taxonomic groups to zoom in and out.

Contents

1. Sampling procedure
2. DNA extraction and library preparation
3. Sequencing
4. Sample description
5. Raw reads data objects
6. Funding
7. Import data
8. Cleaning reads
9. Merge reads
10. Kaiju taxonomic analysis interactive plots

1. Sampling procedure

Please refer to the manuscript for details on the methods and sampling sites.

Bark samples were collected using a sterile knife (aprox. 5 x 5 slices).

Rhizosphere samples were collected with a sterile spoon at Persea americana roots.

Samples were frozen and transported to the laboratory, where they were stored at -80°C.

2. DNA extraction and library preparation

DNA was extracted using a DNeasy PowerSoil kit (QIAGEN). Bark samples were cut in small pieces and inserted directly into the kits vials

Libraries were prepared with a Nextera DNA Flex kit

Seqeuencing was performed on a NextSeq 550 instrument with a 2 x 150 kit.

• A1. Avocado Bark from Malinalco.
• A1. Avocado Bark from Malinalco.
• A1. Avocado Bark from Malinalco.
• SA1. Avocado Rhizospheric Soil from Malinalco.
• SA2. Avocado Rhizospheric Soil from Malinalco.
• SA4. Avocado Rhizospheric Soil from Malinalco.
• SA5. Avocado Rhizospheric Soil from Malinalco.
• A1. Avocado Bark from Morelia.
• A1. Avocado Bark from Morelia.

Instructions to download raw data

1. Sin into KBase at www.kbase.us
2. Go to the KBase narrative at https://narrative.kbase.us/narrative/69195
3. Select the data of interest from the table below.
4. At the data panel at the left, hover on the sample object, and click on "..." to open.
5. Click the download icon to start download.

SEP/CONACyT grant number CB-2014-01-242956

7. Import raw sequence data

Import reads from Sample A1

Import reads from sample A4

Import reads from sample A5

Import reads from sample SA1

Import reads from sample SA2

Import reads from smple SA4

Import reads from ample SA5

Import reads from sample M5

Import reads from ample M6

8. Clean reads with Trimmomatic

Trim reads sample A1.

Bark from Malinalco

Trim reads sample A4.

Bark from Malinalco

Trim reads from sample A5

Bark from Malinalco.

Trim reads from sample SA1

Rhizospheric soil from Malinalco

Trim reads from sample SA2

Rhisospheric soil from Malinalco.

Trim reads from sample SA4

Rhizospheric soil from Malinalco.

Trim reads from sample SA5

Rhizospheric soil from Malinalco.

Trim reads from sample M5

Rhizospheric soil from Morelia.

Trim reads from sample M6

Bark from Morelia.