Illumina sequencing;
large subunit ribosomal RNA gene;
fungal community composition;
phylogenetic community measures;
contrived community analysis;
INTERNAL TRANSCRIBED SPACER;
MAXIMUM-LIKELIHOOD;
COMMUNITIES;
ACCURATE;
CLASSIFICATION;
EVOLUTION;
RESPONSES;
REGION;
TREES;
PLANT;
D O I:
10.1093/femsec/fiv153
中图分类号:
Q93 [微生物学];
学科分类号:
071005 ;
100705 ;
摘要:
The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300-400 bp region of the D2 hypervariable region of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R-LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Together, these findings show that the LR22R-LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Natl Cheng Kung Univ, Inst Informat Management, Tainan, TaiwanBiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Liu, Kuan-Liang
;
Porras-Alfaro, Andrea
论文数: 0引用数: 0
h-index: 0
机构:
Western Illinois Univ, Dept Biol Sci, Macomb, IL 61455 USA
Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Porras-Alfaro, Andrea
;
Kuske, Cheryl R.
论文数: 0引用数: 0
h-index: 0
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Kuske, Cheryl R.
;
Eichorst, Stephanie A.
论文数: 0引用数: 0
h-index: 0
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Eichorst, Stephanie A.
;
Xie, Gary
论文数: 0引用数: 0
h-index: 0
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Natl Cheng Kung Univ, Inst Informat Management, Tainan, TaiwanBiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Liu, Kuan-Liang
;
Porras-Alfaro, Andrea
论文数: 0引用数: 0
h-index: 0
机构:
Western Illinois Univ, Dept Biol Sci, Macomb, IL 61455 USA
Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Porras-Alfaro, Andrea
;
Kuske, Cheryl R.
论文数: 0引用数: 0
h-index: 0
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Kuske, Cheryl R.
;
Eichorst, Stephanie A.
论文数: 0引用数: 0
h-index: 0
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA
Eichorst, Stephanie A.
;
Xie, Gary
论文数: 0引用数: 0
h-index: 0
机构:
Biosci Div, Los Alamos Natl Lab, Los Alamos, NM USABiosci Div, Los Alamos Natl Lab, Los Alamos, NM USA