Abstract
Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium "Candidatus liberibacter asiaticus" (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5-V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.
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Claims 7
Claim · model-written summary
NGS produced 68,722 sequences from citrus test samples.
CitrusOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“As a result, a total number of 68,722 sequences were produced from the test samples.”
e1“bacterial endophytes from citrus leaves”
Claim · model-written summary
Proteobacteria, Firmicutes and Bacteroides were among the most common bacterial endophyte groups in citrus.
- Taxon
- Proteobacteria, Firmicutes, Bacteroides
BacteroidesPseudomonadotaBacillotae0 - Outcome
- most common generae0
- Direction
- most commone0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria.”
e1“bacterial endophytes from citrus leaves”
Claim · model-written summary
Cyanobacteria and Actinobacteria were among the most common bacterial endophyte groups in citrus.
- Taxon
- Cyanobacteria, and ActinobacteriaCyanobacteriotaActinomycetotae0
- Outcome
- most common generae0
- Direction
- most commone0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria.”
e1“bacterial endophytes from citrus leaves”
Claim · model-written summary
C. aurantifolia showed almost equal bacterial diversity to C. paradisi.
- Taxon
- C. aurantifolia
.jpg?width=60)
Citrus ×aurantiifoliae0 - Outcome
- diversitye0
- Direction
- almost equale0
- Comparator
- C. paradisie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e0“C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves.”
Claim · model-written summary
C. reticulata Blanco leaves had a higher proportion of Proteobacteria and Cyanobacteria.
- Taxon
- C. reticulata Blanco
.jpg?width=60)
Citrus reticulatae0 - Organ / stage
- leavese0
- Interactor
- ProteobacteriaPseudomonadotae0other
- Second interactor
- CyanobacteriaCyanobacteriotae0other
- Outcome
- proportion of Proteobacteria and Cyanobacteriae0
- Direction
- highere0
- Comparator
- C. aurantifolia and C. paradisie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e0“C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves.”
Claim · model-written summary
Inverse Simpson indices for microbial abundance in citrus samples were reported as 0.48, 0.567, and 0.163, with sample assignments unresolved.
- Outcome
- abundance of the microbial populatione0
- Value
- 0.48, 0.567, and 0.163e0
- Qualifier
- six different citrus samplese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Schema note from the model: Three index values are given for six samples without identifiable assignments.
Verbatim
e0“According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively.”
Claim · model-written summary
NGS successfully recorded microbiota metagenomics in plant tissues in this citrus study.
- Outcome
- metagenomics of microbiota in plant tissuese0
- Direction
- successfully recordede0
- Setting
- Pakistane1
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology”
e1“16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology”