Background
Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5′-‘TG’–‘CA’-3′ motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures và evolutionary history.
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Results
Here, we report two new LTR-RT subfamilies (TGTT and AACA) with atypical dinucleotide ends of 5′-‘TG’–‘TT’-3′, và 5′-‘AA’–‘CA’-3′ in pear, táo bị cắn, peach & mei. In total, 91 intact LTR-RTs were identified and classified into lớn four TGTT and four AACA families. A structural annotation analysis showed that the four TGTT families, together with AACA1 and AACA2, belong to lớn the Copia-lượt thích superfamily, whereas AACA3 and AACA4 appeared to lớn be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the TGTT1 elements of peach were horizontally transferred from táo bị cắn. In addition, 32 elements from two TGTT and three AACA families had detectable transcriptional activation, & a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs & stress treatments.
Conclusions
Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, và a deep analysis showed their recent activity, horizontal transfer & varied transcriptional levels in different species, organs và căng thẳng treatments. This work enhances our understanding of the structural variation và evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species.
Background
Long terminal repeat retrotransposons (LTR-RTs) are major components that are widespread in flower plant genomes <1>. They are capable of propagating khổng lồ reach thousands of copies in a genome using RNA as an intermediate <2, 3>. LTR-RTs are the most significant contributor khổng lồ genome form size, representing 43% of the nuclear DNA in pear <4>, 38% in táo Apple <5>, 19% in peach <6>, 53% in cotton <7> & over 70% in maize genomes <8>. A representative sầu intact LTR-RT usually contains two highly identical LTRs, which are typically flanked by 2-bp palindromic motifs, commonly 5′-TG–CA-3′. The internal region of an autonomous LTR should contain a primer-binding site (PBS), a polypurine tract (PPT) và two functional genes (gag, and pol) <9>. Based on the order of Reverse transcriptase (rt) và Integrase (int) in pol, LTR-RTs can be further classed inlớn Gypsy and Copia super-families <9>. In addition, the LTR-RTs also contain two types of non-autonomous groups, large retrotransposon derivatives (LARDs) <10> và terminal-repeat retrotransposons in miniature (TRIMs) <11>. The insertion of an LTR-RT is accompanied by the duplication of a 4–6-bp sequence immediately flanking with the 5′ và 3′ ends of the element, called target site duplication (TSD).
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The most comtháng dinucleotide motif flanking the direct LTR-RT repeat regions is the palindromic 5′-TG–CA-3′ motif. However, several LTR-RT families with non-TGCA motifs have sầu been reported. For example, Tos17, a rice LTR-RT that can be activated by tissue culture, has a non-canonical motif of 5′-TG–GA-3′ <12> and TARE1, which was identified as intensively amplified in the tomato lớn genome, ends with 5′-TA–CA-3′ motifs <13>. In addition, AcCOPIA1 that terminated with 5′-‘TG’–‘TA’-3′ at both ends of the LTRs was identified in onion <14>. However, no such non-canonical elements have sầu been identified in the Rosaceae species.
Horizontal transfers (HTs) indicate the transmission of genetic material aý muốn sexually isolated species. As a possible dissemination mechanism of transposable elements (TEs) in eukaryotes, the horizontal transfer of TEs (HTTs) into lớn a new organism is an important step for the TE lớn escape from the silencing machinery of their host genome và obtain a new ‘life cycle’ <15>. The first case of horizontal TE transfer (HTT) was the P TE identified between Drosophila willistoni and Drosophila melanogaster <16>. Recently, with the availability of many plant genome sequences, several HTT cases have sầu been reported mainly through comparative genomic approaches. For example, multiple HTs of the LTR-RT RIRE1 were identified within the genus Oryza <17>, & another LTR-RT family Route66 were found & proven lớn be HTs amuốn the rice, maize & sorghum genomes through a comparative sầu genomics analysis <18>. In addition, 32 HTs of LTR-RTs were discovered by whole genome surveys & comparative analyses in 46 sequenced plant genomes <19>.
The propensity of LTR-RTs not only contributed khổng lồ genome kích thước but also resulted in byproducts of gene disruption, expression level alterations và genomic rearrangements by inserting themselves into lớn genes or their promoter regions <20, 21>. In plants, LTR-RTs are usually silent under normal conditions, but some show transcriptional activities và increased accumulations while under ức chế, potentially triggering the genetic diversity required to lớn evolve adaptations <21, 22>. For example, salternative text (AtCopeg1 in Arabidopsis <23>), drought (BARE1 in barley <24>), heat (ONSEN in Arabidopsis <25, 26>), cold (mPing in rice <27, 28>) và wounding (Corky from Quercus <29>; CLCoy1 in lemon <30>, OARE1 in oat <31> và Tnt1 in tobacteo <32>). Recently, several LTR-RTs were identified as being expressed in the fruits & buds of pear in the RNA-seq databases <33>. However, their study did not focus on the LTR-RTs’ transcription activities under bức xúc in pear.
The Rosaceae family is an economically important angiosperm lineage, containing over 3000 distinct species with chromosome’s numbering from 7 khổng lồ 17 pairs <34>. Some genera with higher economic values that are widely cultivated have had their whole genomes sequenced in the last decade, including pear (Pyrus bretschneideri, n = 17, 527 Mb) <4>, táo (Malus domestica, n = 17, 743 Mb) <5>, peach (Prunus persica, n = 8, 265 Mb) <6>, mei (Prunus mume, n = 8, 280 Mb) <35> và woodl& strawberry (Fragria vesca, n = 7) <36> (Additional file 1: Table S1). Based on DNA sequence data, Fragaria belongs to lớn the Rosoideae, supertribe Rosadea, tribe Potentilleae, Malus & Pyrus occur in the Spiraeoideae, supertribe Pyrodeae, tribe Pyreae and Prunus is in the Spiraeoideae, tribe Amygdaleae <37>. The availability of the five sầu Rosaceae genomic sequences provided opportunities to lớn undertake comparative sầu analyses of LTR-RTs in pear and four other genomes <3, 38>. In this study, a genome wide identification of non-typical LTR-RTs in pear genome was conducted. Two new subfamilies of LTR-RTs, TGTT and AACA, were identified in pear, táo khuyết, peach và mei, but not in strawberry. Their structures, abundance levels, insertion time frames, evolution and transcription activities have been comprehensively analyzed between the four Rosaceae species. TGTT and AACA elements terminate in short inverted repeat dinucleotides, such as ‘TG’ và ‘TT’, ‘AA’ và ‘CA’, & the AACA1 elements in peach may have been horizontally transferred from hãng apple. In addition, multiple elements from the two subfamilies present differential expression levels in different pear organs & also show different expression levels under heat, cold và salt bức xúc treatments. Our study reveals novel structures, horizontal transfer và the transcription activation of two new LTR-RT subfamilies, providing additional information on, and knowledge of, the structure, evolution and activity of TEs in plants.