转座子分布和结构 – 转座子实验室

Distribution of TEs across the eukaryote phylogeny

Reference genome size (sea green circles) varies dramatically across eukaryotes and is loosely correlated with transposable element content. Here, the honey bee TE content is likely an underestimate, as approximately 3% of the genome derives from unusual “large retrotransposon derivatives” (LARDs) (39). For ease of visualisation, DIRS elements have been included with LTRs and all Class II elements included under “DNA”. Data was acquired from genome RepeatMasker output files. Credit to Matt Crook for Volvox carteri silhouette and to Huang et al. for the figure inspiration (71).

Structure and taxonomy of eukaryotic TEs

Left panel: unrooted cladograms showing putative relationships between the major TE superfamilies, based on phylogenies of core protein domains for five subclasses (4, 36, 67, 88, 95, 167). Right panel: genetic structures of representative elements from each subclass. Outlined boxes are open-reading frames, shaded regions are defining protein domains, kinked lines are introns, triangles are repeated sequences and rounded boxes (i.e. for Alu) are RNA elements. Domains with the same colours (excepting gray) indicate shared ancestry. Element lengths not to scale.
Reference: Wells JN, Feschotte C. A Field Guide to Eukaryotic Transposable Elements. Annu Rev Genet. 2020 Nov 23;54:539-561. doi: 10.1146/annurev-genet-040620-022145.

Taxonomic distribution of the 17 DDE Tn superfamilies across the eukaryotic tree of life.

Yuan YW, Wessler SR. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci U S A. 2011 May 10;108(19):7884-9. doi: 10.1073/pnas.1104208108. Epub 2011 Apr 25. PMID: 21518873; PMCID: PMC3093488.

17-superfamilies-eukaryotic-cut-and-paste-DDE domains in fasta format 下载

The assignment of protein domains to DNA TE superfamilies in Fungi

Superfamily	RepBase (Fungi)	Count in RepBase	Yuan and Wessler	DNA TE (with domain)	Observed Distribution	Domains
Academ	Only Puccinia graminis	7	n	9,709	Low copy, in most taxa, highest abundance in Pucciniomycotina	RNase H-like (Yuan and Wessler 2011)
CMC	Basidiomycota and Mucorales	28	y	11,961	Broader distribution, expanded in Agaricomycetes Pucciniomycotina and Mucoromycotina	Transposase_21: PF02992, Transposase_23: PF03017, Transposase_24: PF03004
Dada	Only Laccaria bicolor	2	—	1,023	Broader distribution (4 phyla)	RNase H-like (Kojima and Jurka 2013)
Ginger	Only Malassezia globosa	1	n	6,648	Ubiquitous, expansions in Dikarya	rve: PF00665
hAT	Only Dikarya	37	y	33,376	Ubiquitous	Dimer_Tnp_hAT: PF05699, DUF659: PF04937, DUF4371: PF14291, DUF4413: PF14372
KDZ (Zisupton)	Only Puccinia graminis	4	—	14,607	Basidiomycota, Rhizophagus, Mucoromycotina, and Allomyces	RNase H-like (Iyer et al. 2014)
Kolobok	Only Rhizophagus irregularis	5	n	3,214	Low copy, ubiquitous, highest abundance in R. irregularis	RNase H-like (Yuan and Wessler 2011)
Merlin	Only Rhizopus oryzae	5	y	4,255	Single occurrences in Dikarya, expansions in Microsporidia	DDE_Tnp_IS1595: PF12762
MULE	Dikarya and Rhizopus	36	y	17,658	Ubiquitous	Transposase_mut: PF00872, MULE: PF10551
Novosib	n	0	n	0	Only copies without transposase	—
P	Only Pucciniales & Allomyces	17	y	11	Single occurrences	Tnp_P_element_C: PF12596*, Tnp_P_element: PF12017
PIF/Harb	Diverse Fungi	76	y	13,443	Ubiquitous	Plant_tran: PF04827, DDE_Tnp_4: PF13359
PiggyBac	Mucor and Pezizomycotina	4	y	5,965	Mucoromycota, Microsporidia, and Pezizomycotina	DDE_Tnp_1_7: PF13843
Sola1	n	0	n	140	Rhizophagus, single occurrences in Dikarya	RNase H-like (Majorek et al. 2014)
Sola2	n	0	n	1	One case in Aspergillus flavus	RNase H-like (Majorek et al. 2014)
Sola3	n	0	n	637	Only Rhizophagus	RNase H-like (Majorek et al. 2014)
Tc1/Mariner	Diverse Fungi	148	y	93,120	Ubiquitous	DDE_1: PF03184, DDE_3: PF13358, Transposase_1: PF01359
Transib	n	0	n	0	Absent	RAG1: PF12940
Zator	Only Puccinia striiformis	2	n	1,165	Rhizophagus, single occurrences in Basidiomycota	RNase H-like (Majorek et al. 2014)

Reference: Cut-and-Paste Transposons in Fungi with Diverse Lifestyles | Genome Biology and Evolution | Oxford Academic

Taxonomic distribution of DNA TE superfamilies in major fungal lineages