Table 1.
List of 25 identified OTUs, GenBank accession numbers, their origin, and abundance. In most cases, isolates were grouped based on 98% ITS rDNA sequence similarity and identified using BLAST search.
| OTU identification | Species identification of most homologous sequence from GenBank based on BLAST search* | OTU number | Strain numbers/GenBank numbers | Origin/abundance |
|||
|---|---|---|---|---|---|---|---|
| Stem | Leaf | Root | Seed | ||||
| Diaporthe sp. | Diaporthe cotoneastri (NR 1197261) | (OTU 1) | G111 (KM215632) | 1 | 1 | ||
| Thielavia sp. | Thielavia terricola (AJ271579) | (OTU 2) | G323 (KM215635) | 1 | |||
| Penicillium sp. | Penicillium hispanicum (JX841247) | (OTU 3) | G324 (KM215636) | 1 | |||
| Cladosporium sp | Cladosporium colombiae (NR_119729) | (OTU 4) | G325 (KM215637) | 1 | |||
| Penicillium sp. | Penicillium copticola (NR_1215161) | (OTU 5) | G339 (KM215638) | 1 | |||
| Myrothecium verrucaria | Myrothecium verrucaria (CBS 328.52; AJ302003) | (OTU 6) | G340 (KM215639) | 1 | |||
| Chaetomidium arxii | Chaetomidium arxii (JN709486) | (OTU 7) | G341 (KM215651) | 1 | |||
| Daldinia loculata | Daldinia loculata (AF176959) | (OTU 8) | G343 (KM215641) | 1 | |||
| Zopfiella sp. | Zopfiella longicaudata (GQ922541) | (OTU 9) | G367 (KM215644) | 1 | |||
| Microascus nidicola # | – | (OTU 10) | G377 (KM215645) | 1 | |||
| Trichophaea sp. | Trichophaea hybrida (AF351582) | (OTU 11) | G78 (KM215630)/G379 (KM215647) |
1 | 1 | ||
| Biscogniauxia mediterranea | Biscogniauxia mediterranea (AJ390413) | (OTU 12) | G410 (KM215652) | 1 | |||
| Biscogniauxia atropunctata | Biscogniauxia atropunctata (AJ390411) | (OTU 13) | G411 (KM215648) | 1 | |||
| Penicillium sp. | Penicillium aculeatum (AF033397) | (OTU 14) | G412 (KM215649) | 1 | |||
| Talaromyces minioluteus # | Talaromyces minioluteus (NR_121527.1) | (OTU 15) | G413 (KM215653) | 1 | |||
| Nemania serpens | Nemania serpens (AJ390432) | (OTU 16) | G44 (KM215616) | 1 | |||
| Chaetomium sp | Chaetomium rectangulare (HM365239) | (OTU 17) | G45 (KM215617) | 1 | |||
| Penicillium sp. | Penicillium restrictum (NR_121239) | (OTU 18) | G342 (KM215640) | 1 | |||
| Alternaria sp. | Alternaria metachromatica (AY762946) | (OTU 19) | G54 (KM215621)/G58 (KM215625)/G59 (KM215626)/G60 (KM5215627)/G62 (KM5215628)/G63 (KM5215629) |
6 | |||
| Alternaria sp. | Alternaria eichhorniae (NR_111832) | (OTU 20) | G40 (KM215615)/G47 (KM215618)/G48 (KM215619)/G57 (KM215624)/G378 (KM215646) |
4 | 1 | ||
| Alternaria sp. | Alternaria dauci ((NR_077186) | (OTU 21) | G49 (KM215620)/G50 (KM215650)/G55 (KM215622)/G56 (KM215623) |
4 | |||
| Fusarium sp. | Fusarium fujikuroi (NR_111889) | (OTU 22) | G344 (KM215642)/G345 (KM215643) |
2 | |||
| Penicillium restrictum # | Penicillium restrictum (NR_121239) | (OTU 23) | G85 (KF367458) | 1 | |||
| Acremonium sp. | Acremonium sclerotigenum (FN706552) | (OTU 24) | G246 (KM215633)/G248 (KM215634) |
2 | |||
| Aspergillus iizukae # | Aspergillus iizukae (EF669597) | (OTU 25) | G77 (AB859956)/G82 (KM215631) |
1 | 1 | ||
Notes: *Fungal endophyte OTUs were tentatively assigned to either genus or species by matching the most homologous sequences in GenBank by BLAST search. Where possible, only authentic sequences (RefSeq) were used for assigning OTUs preferentially from type or other authentic cultures generated by taxonomic specialist published in high impact factor Mycology journals. When multiple species were found to have high sequence similarity or when <98% sequence homology was found with a published authentic sequence for which a culture was deposited in a public culture collection, we choose to take a more conservative approach and use only the genus name for OTU assignment. Furthermore, most OTU identifications were corroborated via their higher level phylogenetic placement using a portion of partial LSU sequence (D1/D2 region) (see Fig S8, Supporting Information).
For OTU names followed by ‘#’ symbol, we used morphological characteristics of conidia or teleomorph formed in culture as well as sequence data from portions of partial LSU gene sequences (D1/D2) region and/or protein coding data in addition to ITS data in separately published studies by our research group to confirm OTU identification.