Seed-borne bacterial diversity of oat and functional analysis based on Illumina MiSeq high-throughput sequencing

doi:10.11686/cyxb2022427

Abstract

Abstract:

In this study， the high-throughput sequencing analysis method was used to analyze the difference in bacterial abundance， alpha diversity， beta diversity and species composition of bacterial communities in seven oat varieties from different regions. The PICRUSt and FAPROTAX functional prediction methods were used to analyze the differences in abundance among the seed-borne bacteria in various bands. The results showed： 1） A total of 5187 bacterial OTUs were obtained from the seven oat varieties， mainly belonging to 33 phyla， 180 orders and 435 genera. 2） Based on the abundance and annotation information of the OTUs， we found that Proteobacteria， Chloroflexbacteria， Cyanobacteria and Actinobacteria were the dominant phyla in the bacterial communities of the seven oat varieties. At the order level， the most abundant groups were Rickettsiales and Sphingomonadales. Dominant genera were Sphingomonas， Solibacter and Pseudarthrobacter. 3） The results of α diversity and β diversity analysis suggest that the bacterial community diversity and community structure of different oat varieties were quite different. Notably， variety LXY-5 had the largest alpha diversity. Additionally， LEFSe analysis further showed that the biomarkers differed by species for different oat cultivars. 4） The functional prediction analysis using PICRUSt and FAPROTAX showed that the bacterial community in the oat seed samples mainly comprised three metabolic categories： metabolism， organic systems and human diseases， which could be classified into 42 KEGG and 24 COG secondary metabolic pathways. Moreover， a total of 52 metabolic pathways were obtained after FAPROTAX functional annotation. This study provides a theoretical basis for clarifying the diversity of the bacterial load of oat seed， and potentially can contribute to development of new genetic resources.

Key words: Illumina MiSeq high-throughput sequencing, oat seed-borne bacteria, bioinformatics analysis, PICRUSt, FAPROTAX

Zhen-fen ZHANG, Rong HUANG, Xiang-yang LI, Bo YAO, Gui-qin ZHAO. Seed-borne bacterial diversity of oat and functional analysis based on Illumina MiSeq high-throughput sequencing[J]. Acta Prataculturae Sinica, 2023, 32(7): 96-108.

Figures/Tables 9

References 44

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编号 Code	燕麦品种 Oat varieties	产地 Production region	地理位置 Geographical location	储存年限 Storage year （year）
LXY-1	甜燕麦 Sweet oat	青海西宁 Xining， Qinghai	92°35′ E， 38°26′ N	9
LXY-2	燕麦473 Oat 473	甘肃通渭 Tongwei， Gansu	105°0l′ E， 35°23′ N	5
LXY-3	白燕7号 Baiyan No. 7	甘肃通渭 Tongwei， Gansu	105°0l′ E， 35°23′ N	5
LXY-4	贝勒2代 Baler 2	加拿大 Canada	121°50′ E， 43°83′ N	5
LXY-5	陇燕2号 Longyan No.2	甘肃山丹Shandan， Gansu	101°08′ E， 38°78′ N	6
LXY-6	陇燕4号 Longyan No.4	甘肃天祝 Tianzhu， Gansu	102°79′ E， 37°21′ N	5
LXY-7	陇燕5号 Longyan No.5	甘肃定西 Dingxi， Gansu	104°59′ E， 35°56′ N	5

编号 Code	燕麦品种 Oat varieties	产地 Production region	地理位置 Geographical location	储存年限 Storage year （year）
LXY-1	甜燕麦 Sweet oat	青海西宁 Xining， Qinghai	92°35′ E， 38°26′ N	9
LXY-2	燕麦473 Oat 473	甘肃通渭 Tongwei， Gansu	105°0l′ E， 35°23′ N	5
LXY-3	白燕7号 Baiyan No. 7	甘肃通渭 Tongwei， Gansu	105°0l′ E， 35°23′ N	5
LXY-4	贝勒2代 Baler 2	加拿大 Canada	121°50′ E， 43°83′ N	5
LXY-5	陇燕2号 Longyan No.2	甘肃山丹Shandan， Gansu	101°08′ E， 38°78′ N	6
LXY-6	陇燕4号 Longyan No.4	甘肃天祝 Tianzhu， Gansu	102°79′ E， 37°21′ N	5
LXY-7	陇燕5号 Longyan No.5	甘肃定西 Dingxi， Gansu	104°59′ E， 35°56′ N	5

样本Sample	Chao1指数Chao1 index	Shannon指数Shannon index	Simpson指数Simpson index	覆盖率Coverage （%）
LXY-1	2861.71±97.59b	7.44±0.92b	0.94±0.04a	96.89±0.01a
LXY-2	2913.72±85.14ab	7.98±0.43ab	0.96±0.02a	96.99±0.01a
LXY-3	2921.24±194.41ab	7.83±0.74ab	0.96±0.02a	96.86±0.01a
LXY-4	2967.91±54.39ab	8.56±0.45ab	0.98±0.01a	97.02±0.01a
LXY-5	3057.15±13.84a	8.61±0.62ab	0.98±0.02a	96.94±0.01a
LXY-6	2974.10±101.12ab	8.53±0.59ab	0.98±0.02a	97.00±0.01a
LXY-7	3064.78±28.90a	8.68±0.26a	0.98±0.01a	96.92±0.01a

样本Sample	Chao1指数Chao1 index	Shannon指数Shannon index	Simpson指数Simpson index	覆盖率Coverage （%）
LXY-1	2861.71±97.59b	7.44±0.92b	0.94±0.04a	96.89±0.01a
LXY-2	2913.72±85.14ab	7.98±0.43ab	0.96±0.02a	96.99±0.01a
LXY-3	2921.24±194.41ab	7.83±0.74ab	0.96±0.02a	96.86±0.01a
LXY-4	2967.91±54.39ab	8.56±0.45ab	0.98±0.01a	97.02±0.01a
LXY-5	3057.15±13.84a	8.61±0.62ab	0.98±0.02a	96.94±0.01a
LXY-6	2974.10±101.12ab	8.53±0.59ab	0.98±0.02a	97.00±0.01a
LXY-7	3064.78±28.90a	8.68±0.26a	0.98±0.01a	96.92±0.01a

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