TreeBASE Search-Matrix 38374 of study 19714

@ARTICLE{TreeBASE2Ref26204, author = {Justin P Shaffer and Carolina Sarmiento and Paul-Camilo Zalamea and Rachel Elizabeth Gallery and Adam S Davis and David A Baltrus and A. Elizabeth Arnold}, title = {Diversity, specificity, and phylogenetic relationships of endohyphal bacteria in fungi that inhabit tropical seeds and leaves}, year = {2016}, keywords = {Ascomycota, Barro Colorado Island, Cecropia, endobacteria, phylogenetic diversity, pioneers, symbiosis}, doi = {10.3389/fevo.2016.00116}, url = {http://}, pmid = {}, journal = {Frontiers in Ecology and Evolution}, volume = {4}, number = {116}, pages = {}, abstract = {Interactions between fungi and tropical trees are responsible for some of the most biodiverse communities on earth. These interactions occur in the presence of additional microbes that can modify fungal phenotypes, such as endohyphal bacteria. Here we examine the occurrence, diversity, and composition of endohyphal bacteria (EHB) in fungi that colonize seeds and leaves of plants in tropical forests. We use PCR and visual fluorescence to detect EHB among fungi, and a phylogenetic approach to explore the evolutionary relationships among seed- and leaf-inhabiting fungi and their bacterial partners. Analyses focusing on two prevalent orders of fungi (Hypocreales and Xylariales) revealed that seed- and leaf-inhabiting fungi have a shared evolutionary history, yet differ in the prevalence, richness, and composition of their endohyphal symbionts. Phylogenetic analyses detected that the EHB habit is widespread, here encompassing members of seven phyla of bacteria (including three classes of Proteobacteria). Occurring in seed- vs. leaf-associated fungi has not resulted in detectable structure in the evolution of EHB, and no congruence was observed in the phylogenetic relationships of these apparently facultative, horizontally transmitted symbionts. Our results are consistent with multiple origins of fungus-bacterium associations and argue for evaluating focal pairs to determine how particular EHB affect the establishment or maintenance of fungal symbioses in seeds and leaves.} }

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Matrix 38374 of Study 19714

Citation title: "Diversity, specificity, and phylogenetic relationships of endohyphal bacteria in fungi that inhabit tropical seeds and leaves".

Study name: "Diversity, specificity, and phylogenetic relationships of endohyphal bacteria in fungi that inhabit tropical seeds and leaves".

This study is part of submission 19714 (Status: Published).

Matrices

Title: Lactobacillales / Firmicutes

Description: 16S rRNA

Rows

Taxon Label	Row Segments	Characters 1?–30
9731_cl07_Xylaria__C._insignis_BCI-BCI_{12}__NR_042776.1_*_z	(none)	CCGCATAACAATGGATGACTCATGTCATTT
P0079_Xylaria__P._limonensis_BCI__NR_042248.1_*_ad	(none)	CCGGATAACCCGTGCCACCTCATGGAGGGG
Lactobacillus_nagelii_*_NR_119275.1	(none)	CCGCATAACCACAGAAACCACATGGTTTCT
Facklamia_languida_*_NR_026487.1	(none)	CCGCATAGAATCACAGATC?CATGATCAAT
P0305_cl04_Fusarium__X._macrantha_BCI__NR_026487.1_*_j	(none)	CCGCATAGAATCACAGATCGCATGATCAAT
Globicatella_sulfidifaciens_*_NR_025437.1	(none)	CCGCATAGACAATTTAACCGCCTGGTTAAG
P0362_cl01_Xylaria__S._panamensis_BCI__NR_025437.1_*_w	(none)	CCGCATAGACAATTTAACCGCCTGGTTAAA
Aerococcus_urinaehominis_*_NR_028922.1	(none)	CCGCATAGTAATCCATGTCGCATGACAGGG
Bacillus_lentus_*_NR_040792.1	(none)	CCGGATAACTTCTTTCTTCTCCTGGAGAAA
Bacillus_megaterium_*_NR_043401.1	(none)	CCGGATAGGATCTTCTCCTTCATGGGAGAT
Granulicatella_elegans_*_NR_028682.1	(none)	CCGCATAGGTTCTTTAGTCGCATGACTGAA
P0538_cl14_Fusarium__C._argentum_BCI__AY879301.1_*_j	(none)	CCGCATAGGTCTTCGAACCGCATGGTTTGA
Granulicatella_para-adiacens_*_AY879301.1	(none)	CCGCATAGGTCTTCGAACCGCATGGTTTGA
P0392_cl12_Xylaria__P._reticulatum_BCI__AY879301.1_*_w	(none)	CCGCATAGGTCTTCGAACCGCATGGTTTGA
Carnobacterium_sp._BBDP71_*_DQ337531.1	(none)	CCGCATAACTCCAACCACCTCCTGGTGGAT
Alkalibacterium_iburiense_*_dbj_AB294177.1	(none)	CCGCATAGGTATCCGACACGCATGTGTCGG
Alkalibacterium_pelagium_*_NR_041574.1	(none)	CCGCATAGGTGATCATAGCGCATGCTTAGA
P0842_Xylaria__C._pelatata_BCI__NR_042248.1_*_w	(none)	CCGGATAACCCGTGCCTCCTCCTGGAGGCG
Atopococcus_tabaci_*_NR_042248.1	(none)	CCGGATAACCCGTGCCTCCTCCTGGAGGCG
P0305_cl01_Fusarium__X._macrantha_BCI__DQ337531.1_*_j	(none)	CCGGATAACCCGTGCCTCCTCCTGGAGGCG
P0392_cl06_Xylaria__P._reticulatum_BCI__NR_040792.1_*_w	(none)	CCGGATAACCCGTGCCTCCTCCTGGAGGCG
P0199_cl08_Xylaria__C._cainito_BCI__NR_040792.1_*_w	(none)	CCGGATAACCCGTGCCTCCTCCTGGAGGCG
P0857_cl10_Xylaria__Parmeliaceae1_BCI__AB294177.1_*_w	(none)	CCGGATAACCCGTGCCTCCTCCTGGAGGCG
Lactovum_miscens_*_AJ439543	(none)	CCGCATAAAAGAAGGCTTCACATGAAGCCA
Lactococcus_lactis_subsp._lactis_*_NR_103918.1	(none)	CCGCATAAAAACTTTAAACACAAGTTTTAA
PS0965_Fusarium__A._spraguei_BCI_Armour-SE__NR_103918.1_*_a	(none)	CCGCATAAAAACTTTAAACACAAGTTTTAA
9902_Fusarium__C._insignis_BCI-BCI_{09}__JQ687117.1_*_e	(none)	CCGCATAACAATGGATGACACATGTCATTT
P0242_cl09_Xylaria__H._prunifolius_BCI__AB200871.1_*_w	(none)	CCGCATAACAATGGATGACACATGTCATTT
Streptococcus_thermophilus_*_dbj_AB200871.1	(none)	CCGCATAACAATGGATGACACATGTCATTT
P0848_cl12_Xylaria__Parmeliaceae1_BCI__FR873482.1_*_w	(none)	CCGCATAACAATGGATGACACATGTCATTT
Streptococcus_salivarius_*_NR_042776.1	(none)	CCGCATAACAATGGATGACACATGTCATTT
Streptococcus_sp_*_JQ687117.1	(none)	CCGCATAACAATGGATGACACATGTCATTT
P0265_cl03_Fusarium__H._prunifolius_BCI__NR_074109.1_*_j	(none)	CCGCATAACAGTAGATATTGCATGATATCT
Streptococcus_parasanguinis_*_NR_074109.1	(none)	CCGCATAAAAGTCGACATTGCATGATGTTG
Streptococcus_sp._*_HM596298.1	(none)	CCGCATAAAATGGATTATCGCATGATGATT
Streptococcus_mitis_*_AY518677.1	(none)	CCGCATAAGAGTAGATGTTGCATGACATTT
Streptococcus_pseudopneumoniae_*_NR_074987.1	(none)	CCGCATAAGAGTAGATGTTGCATGACATTT
Streptococcus_sanguinis_*_CP000387.1_16379-17929	(none)	CCGCATAAAATTGATTATTGCATGATAATT
P0160_cl03_Xylaria__H._prunifolius_BCI__CP000387.1_*_w	(none)	CCGCATGATATTAATTGTCGCATGATAATT
P0392_cl15_Xylaria__P._reticulatum_BCI__CP000387.1_*_w	(none)	CCGCATAAAATTGATTATTGCATGATAATT

Columns

None of the columns has a description.