Diaspora, a large family of Ty3-gypsy retrotransposons in Glycine max, is an envelope-less member of an endogenous plant retrovirus lineage

Abstract

Background: The chromosomes of higher plants are littered with retrotransposons that, in many cases, constitute as much as 80% of plant genomes. Long terminal repeat retrotransposons have been especially successful colonizers of the chromosomes of higher plants and examinations of their function, evolution, and dispersal are essential to understanding the evolution of eukaryotic genomes. In soybean, several families of retrotransposons have been identified, including at least two that, by virtue of the presence of an envelope-like gene, may constitute endogenous retroviruses. However, most elements are highly degenerate and are often sequestered in regions of the genome that sequencing projects initially shun. In addition, finding potentially functional copies from genomic DNA is rare. This study provides a mechanism to surmount these issues to generate a consensus sequence that can then be functionally and phylogenetically evaluated.

Results: Diaspora is a multicopy member of the Ty3-gypsy-like family of LTR retrotransposons and comprises at least 0.5% of the soybean genome. Although the Diaspora family is highly degenerate, and with the exception of this report, is not represented in the Genbank nr database, a full-length consensus sequence was generated from short overlapping sequences using a combination of experimental and in silico methods. Diaspora is 11,737 bp in length and contains a single 1892-codon ORF that encodes a gag-pol polyprotein. Phylogenetic analysis indicates that it is closely related to Athila and Calypso retroelements from Arabidopsis and soybean, respectively. These in turn form the framework of an endogenous retrovirus lineage whose members possess an envelope-like gene. Diaspora appears to lack any trace of this coding region.

Conclusion: A combination of empirical sequencing and retrieval of unannotated Genome Survey Sequence database entries was successfully used to construct a full-length representative of the Diaspora family in Glycine max. Diaspora is presently the only fully characterized member of a lineage of putative plant endogenous retroviruses that contains virtually no trace of an extra coding region. The loss of an envelope-like coding domain suggests that non-infectious retrotransposons could swiftly evolve from infectious retroviruses, possibly by anomalous splicing of genomic RNA.

Figure 1

Histogram of local densities of Genbank Accessions used to construct a Diaspora consensus contig. Recognition sites of restriction enzymes used to generate BAC libraries are indicated. Restriction sites in () are found in < 50% of sequences. The right LTR is not shown. The contig was assembled from the following Genbank Accessions: AF095730 (this study), AY656632-AY656656 (this study), AY656659-AY656662 (this study), AQ989187, AQ989208, AQ989232, AQ989271, AQ989295, AZ044709, AZ045083, AZ221405, AZ301361, AZ302029, AZ536637, AZ933330, AZ936131, BE611677, BH000863, BH000924, BH001187, BH023628, BH023632, BH023632, BH173556, BH405523, BH405626, BH405659, BH405669, BH610143, BH610157, BH610193, BH840834, BH854486, BH888573, BH897988, BH912698, BI974271, BU546431, CC062189, CC062259, CC062269, CC062279, CC062321, CC062333, CC062399, CC062412, CC062425, CC062501, CC062524, CC062576, CC062745, CC062865, CG811196, CG812831, CG813036, CG813244, CG813336, CG813336, CG813447, CG813495, CG813591, CG813669, CG813710, CG813854, CG813944, CG814001, CG814027, CG814297, CG814428, CG814537, CG814691, CG814705, CG814739, CG814773, CG814814, CG814837, CG814944, CG814960, CG815296, CG815349, CG815376, CG815566, CG815593, CG815931, CG815990, CG816077, CG816195, CG816437, CG816499, CG816820, CG816902, CG816924, CG816965, CG817175, CG817237, CG817248, CG817294, CG817426, CG817444, CG817647, CG817665, CG817749, CG817754, CG817777, CG817807, CG817873, CG817996, CG818405, CG818428, CG818443, CG818626, CG818673, CG818711, CG819087, CG819204, CG819222, CG819552, CG819604, CG819672, CG819766, CG819790, CG819813, CG819936, CG819977, CG820067, CG820103, CG820158, CG820299, CG820411, CG820560, CG820627, CG820654, CG820656, CG820670, CG820673, CG820702, CG820718, CG820816, CG820848, CG820850, CG820868, CG821026, CG821085, CG821093, CG821150, CG821179, CG821206, CG821219, CG821294, CG821311, CG821532, CG821597, CG821693, CG821710, CG821772, CG821963, CG822140, CG822195, CG822264, CG822361, CG822369, CG822426, CG822466, CG822466, CG822582, CG823113, CG823202, CG823294, CG823320, CG823499, CG823505, CG823511, CG823713, CG824266, CG824332, CG824372, CG824380, CG824407, CG824533, CG825062, CG825163, CG825591, CG825777, CG825811, CG825933, CG826013, CL867862, CL8811208, CL881708, CL882298, CL886562, CL891285, CL899081

Figure 2

A. Consensus nucleotide sequence of Diaspora. LTR in red, PBS in green, ORF in blue, PPT in maroon. B. Structural organization of Diaspora. PBS: tRNA primer binding site; Gag: Gag core domain (CDD17379); Z: CCHC Zn finger domain; P: protease catalytic core; RT: reverse transcriptase core domain (CDD16610); Int: integrase core domain (CDD25582); PPT: polypurine tract. (⇨) ORF. Consensus restriction sites as in Fig. 2 H: HindIII; E: EcoRI; B: BamHI.

Figure 3

Conceptual translation of the Diaspora ORF. Teal: Gag core domain; blue: Zn finger domain; red: protease catalytic core; green: RT core domain; violet: integrase core domain

Figure 4

Base pairing of PBS (upper case) from Diaspora and Calypso with the 3' end of tRNA^Asp. LTR terminus underlined.

Figure 5

Neighbor-joining phylogenetic tree using p-distances based on conserved RT domains 2 through 7 [29] of gypsy-like LTR retroelements from higher plants. The tree is rooted to gypsy. Bootstrap values from 1000 pseudo-replicates shown as percentages only at nodes with > 50% support. Vertical line indicates genus; key below. Named elements followed by Genbank Accession numbers; unnamed elements designated by Accession Number and, for translated nucleotide sequences, first nucleotide position. Wilma 634M12: AY494981 [51]; Wilma 426K20: AY146588 [51]; Wilma 107M9: AY368673 [51]; BAGY-2: AJ279072 [13]; Tmt1-1: AC146683 (115510-125622); Athila4-1: AC007209 [10]; Athila6-1: AF104920 [10]; Athila1-1: AB005248 [52]; Athila5-1: AF147260 [10]; AP005726: 133249; AC136972: 155124; Calypso2-1: AF186183 [10]; Calypso3-1: AF186185 [10]; Calypso5-1: AF186186 [10]; Calypso4-1: AF186185 [10]; Cyclops-1: AJ000639 [8]; AP004896: 78828; Tlc1-1: AP006432 (23839-35862); Tlc1-2: AP006350 (29612-19200); BBRE1: T12085; TfcII sr1: AF219199; TfcII sr25: AF219208; TfcII sr18: AF219207; cot8-6: AF378037 [10]; cot5-3: AF378037 [10]; cot8-7: AAL06412 [10]; Tpb1-1: AC149297 (90224-102138); syc2-3: AF378052 [10]; syc4-2: AF378053 [10]; DiasporaLc: AP007806: 43868; Tat4-1: AB005247 [44]; Cinful-1: AF049110 [45]; Grande1-4: X97604 [46]; RIRE2: AB030283 [47]; Reina: U69258 [48]; Cereba: AY040832 [49]; RIRE7: BAA89466 [50]; RIRE7-2: AL731604 (96205-102279); Dea1: T07863 [51]; del1-46: X13886 [52]; BAGY-1: Y14573 [27]; Tekay: AAL59229 [53]; RIRE3-2: AC123974 (48149-59938); RIRE3: AB014738 [50]; Retrosat2: AAM74400; Retrosat2-2: AL662955 (58578-70224); Gypsy: P10401 [54]. ^aTriticum; ^bHordeum; ^cMedicago; ^dArabidopsis; ^eOryza; ^fGlycine; ^gPisum; ^hLotus; ⁱVicia; ^jFritillaria; ^kGossypium; ^lPopulus; ^mPlatanus; ⁿZea; ^oAnanas; ^pLilium; ^qSorghum; ^rDrosophila

Figure 6

Structural organization of Athila, Calypso, and Diaspora consensus elements.