草业学报 ›› 2023, Vol. 32 ›› Issue (7): 96-108.DOI: 10.11686/cyxb2022427
张振粉1,2(), 黄荣1,2, 李向阳1,2, 姚博1,2, 赵桂琴1,2
收稿日期:
2022-10-27
修回日期:
2022-11-26
出版日期:
2023-07-20
发布日期:
2023-05-26
通讯作者:
张振粉
作者简介:
张振粉(1984-),男,福建霞浦人,副教授,博士。E-mail: zhangzf@gsau.edu.cn基金资助:
Zhen-fen ZHANG1,2(), Rong HUANG1,2, Xiang-yang LI1,2, Bo YAO1,2, Gui-qin ZHAO1,2
Received:
2022-10-27
Revised:
2022-11-26
Online:
2023-07-20
Published:
2023-05-26
Contact:
Zhen-fen ZHANG
摘要:
采用高通量测序法,分析 7 份来自不同地区的燕麦种带细菌群落的细菌丰度、Alpha多样性、Beta多样性和物种组成差异,并采用 PICRUSt和FAPROTAX功能预测的方法分析了各种带细菌间的丰度差异。结果显示:1)7份燕麦中共获得5187个细菌可操作分类单元(OTUs),主要归属于33个门、180个目和435个属。2)基于OTUs的丰度及注释信息,7份燕麦种带细菌群落中变形菌门、绿弯菌门、酸杆菌门、放线菌门和蓝菌门为优势菌门,立克次氏体目和鞘脂单胞菌目为优势菌目,鞘氨醇单胞菌属、Solibacter和假节杆菌属为优势菌属。3) Alpha多样性和Beta多样性表明不同燕麦品种的细菌群落多样性和群落结构具有较大差异,其中 LXY-5 具有最大的Alpha多样性。LEFSe分析更进一步显示不同的燕麦品种生物标记的物种不同。4) PICRUSt 和 FAPROTAX 功能预测分析表明,燕麦种带细菌群落主要有代谢、有机系统和人类疾病3个代谢通路,分属于有42个 KEGG 和24个COG的二级代谢途径;FAPROTAX功能注释后共获得52个生态功能。研究结果为明确燕麦种带细菌多样性及开发新型基因资源提供了理论依据。
张振粉, 黄荣, 李向阳, 姚博, 赵桂琴. 基于Illumina MiSeq高通量测序的燕麦种带细菌多样性及功能分析[J]. 草业学报, 2023, 32(7): 96-108.
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.
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 |
表1 供试种样的来源及相关信息
Table 1 Origin and information of tested seed samples
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 |
表2 7个燕麦品种的种带细菌群落Alpha多样性指数
Table 2 Alpha diversity index of seed-borne bacterial community in 7 oat cultivars
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 |
图4 燕麦种带细菌线性判别分析a: 物种进化分支图Evolutionary clade of species; b: 显著差异物种 LDA 值分布柱状图,筛选标准为P<0.05, LDA值>3。P <0.05 and LDA>3 were the screening criteria for linear discriminant analysis of significantly different species.
Fig.4 Linear discriminant analysis of oat seed-borne bacteria
图5 不同燕麦品种种带细菌KEGG功能多样性热图颜色深浅表示代谢功能表达量与均值的差异程度。以同一样本基因表达量平均值为基准,高于平均值表达量则为正值,标记为红色;反之,低于平均值表达量则为负值,标记为蓝色,下同。Color shades indicate the degree of difference between the expression of metabolic function and the mean. The average value of gene expression in the same sample is used as the benchmark, and the expression above the average is positive, and the mark is red; Conversely, the expression below the average is a negative value and marked as blue, the same below.
Fig.5 Heat map of seed-borne bacteria KEGG functional diversity in different oat varieties
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