Phylogenetically structured differences in rRNA gene sequence variation among species of arbuscular mycorrhizal fungi and their implications for sequence clustering

บทความในวารสาร

ผู้เขียน/บรรณาธิการ

วิทยา เขาหนองบัว

กลุ่มสาขาการวิจัยเชิงกลยุทธ์

ไม่พบข้อมูลที่เกี่ยวข้อง

รายละเอียดสำหรับงานพิมพ์

รายชื่อผู้แต่ง: House G.L., Ekanayake S., Ruan Y., Sch�tte U.M.E., Kaonongbua W., Fox G., Ye Y., Bevera J.D.

ผู้เผยแพร่: American Society for Microbiology

ปีที่เผยแพร่ (ค.ศ.): 2016

วารสาร: Applied and Environmental Microbiology (0099-2240)

Volume number: 82

Issue number: 16

หน้าแรก: 4921

หน้าสุดท้าย: 4930

จำนวนหน้า: 10

นอก: 0099-2240

eISSN: 1098-5336

URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84982128228&doi=10.1128%2fAEM.00816-16&partnerID=40&md5=9bb2b98ee36c58c669d9816bdef766bf

ภาษา: English-Great Britain (EN-GB)

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บทคัดย่อ

Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. ฉ 2016, American Society for Microbiology.

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