Searching for active mobile genetic elements in dsRNA fraction of Pinus sylvestris having witches broom abnormalities

Abstract

The most common type of coniferous mobile genetic elements are retrotransposons. Despite of their early positive impact on evolution of modern coniferous species they can have a significant negative impact for Forestry and breeding. Breaking genomic structural integrity mobile elements can cause phenotypic defects of plants. In this regard, the study of the diversity of coniferous mobile genetic elements is particularly interesting. In the present paper, we describe mobile genetic elements in dsRNA fraction of Pinus sylvestris having witches broom abnormalities. In result of assembled contigs analysis by RepeatMasker 70 mobile genetic elements were identified. A 68 of that were retroelements. Most of elements represented by Gypsy (16 contigs) and Copia (48 contigs). In 4 cases retroelements specific to Pinus taeda were identified. In most cases fragments of integrase (24), reverse transcriptase (22) and RNaseH (15) were identified. Results of the study may be of interest for coniferous breeding and genetic specialists.

The raw data of these experiments have been deposited at NCBI under the accession number SAMN06185845.

Specifications
Organism/cell line/tissue	Scots pine
Sex	NA
Sequencer or array type	Ion PGM (Thermo Scientific, USA)
Data format	Normalized and processed microarray data, qPCR data
Experimental factors	dsRNA fraction of Scots pine shoots tissue with signs of “witches broom”
Experimental features	The data were obtained on dsRNA fraction sequenced at Ion PGM
Consent	NA
Sample source location	SFI “Korenevskaya Experimental Forest Enterprise of NAS of Belarus” Gomel, Belarus.

1. Introduction

In coniferous plants retrotransposons make up a large part of the genome [1], [2]. It is estimated that 70% of the genetic material is repetitive genetic elements. About 58% among it of the genome constitute LTR-containing retrotransposons (35% Group Ty3/Gypsy, 16% a group of Ty1 / Copia, 7% is not classified), 1% - the LINE-elements, 1% - DNA transposons, 10% - unclassified high copy number DNA [3]. Mobile genetic elements played an important role in the evolution of conifers genomes [3], [4]. However, the virus-like genetic elements (or retrotransposons) have a negative value for forestry, because of their displacement and insertions they cause different disturbances to structural and functional organization of the genome [5]. On the other hand, virus-like mobile genetic elements are a reservoir of natural variation and play an important role in macroevolution processes [6]. Studies of retrotransposons could shield light to complexity of its regulation to develop methods of transposon\destabilisation depending on breeding program needs.

2. Experimental design, materials and methods

2.1. Pine and spruce sampling and processing

Samples of the Scots pine (Pinus sylvestris L.) were collected in forest stands around the Homiel town (52°26′43″N and 30°59′03″E), which is located about 40 km from the southeastern border of the Republic of Belarus. Pine samples were green shoots (with needles) of witch’s brooms (21 pcs. from individual trees), spruce samples were green shoots of pineapple galls, produced by Adelges abietis L. (6 pcs. from individual trees). Samples were dissected with thin scalpels under a stereomicroscope (Leica M50, Leica Microsystems GmbH, Germany). Inner tissues was carefully separated from the coating surrounding tissues, and quickly transferred to microtubes containing RNAlater solution (Thermo Scientific, U.S.A.).

2.2. RNA isolation and ds cDNA pool preparation

Total RNA was prepared using the GeneJet Plant RNA Purification Mini Kit (Thermo Scientific, U.S.A.), which is based on a combination of guanidine-isothiocyanate lysis and silica-membrane purification in a mini-spin column. The procedures were performed according to the manufacturer's instructions. The quality of the RNA was analyzed with denaturating RNA electrophoresis in 1 × TAE 1% agarose gel and quantified by UV absorption using Implen P330 (Implen GmbH, Germany).

The ds cDNA pool was prepared using Maxima H Minus Double-Stranded cDNA Synthesis Kit (Thermo Scientific, U.S.A.). Briefly, the synthesis of first strand cDNA began with 1 μg of total RNA and 0.5 μg random hexanucleotide primers. The resulting first strands of cDNA (RNA-DNA hybrid molecule) were processed with enzyme mix of E. coli RNase H, DNA polymerase I and DNA ligase immediately. E. coli RNase H inserted nicks into the RNA, providing 3′ OH-primers for DNA polymerase I. The 5′–3′ exonuclease activity of E. coli DNA polymerase I removed the RNA strand in the direction of synthesis, while its polymerase activity replaced the RNA with deoxyribonucleotides. DNA ligase linked the gaps to complete the ds cDNA strand. The quality of the ds DNA was analyzed with electrophoresis in 1 × TBE 1.5% agarose gel and quantified by UV absorption using Implen P330 (Implen GmbH, Germany).

2.3. cDNA library preparation and deep Sequencing using Ion Torrent Technology

A fragment library was generated with an input of 100 ng ds cDNA using the Ion Xpress Plus Fragment Library Kit (Thermo Scientific, U.S.A.). Next, DNA fragmentation, adaptor ligation, fragment size selection and library amplification were carried out according to manufacturer's instructions. The targeting of fragments of approximately 330 bp was performed with 1.5 × TBE 2% agarose gel (Helicon, Russia). Prior to emulsion PCR, the size distribution were assessed with 1.5 × TBE 2% agarose gel (Helicon, Russia); concentrations of the libraries were normalized with Ion Library Equalizer Kit (Thermo Scientific, USA). The fragment library was adjusted to approximately 26 pM and amplified with Ion Sphere particles™ (ISPs) by emulsion PCR using the Ion OneTouch™ Instrument with the Ion OneTouch™ 200 Template Kit (Thermo Scientific, USA) and template-positive ISP enrichment according to the manufacturer's protocol (Thermo Scientific, USA). About 50% of the ISPs were and then sequenced on an Ion 314™ chip using the Ion Torrent Personal Genome Machine (PGM™) (Thermo Scientific, USA) for 130 cycles (520 flows) with the Ion PGM™ 200 Sequencing Kit (Thermo Scientific, USA). Initial processing of ION PGM data carried out in an automatic mode using Ion Torrent Suite (Thermo Scientific, USA) software.

2.4. Sequence filtering and (de novo) assembly of deep sequencing data

Ion Torrent Personal Genome Machine (Thermo Scientific, USA) sequencing can generate processed reads 200–260 base length for analyzed cDNA fragments.

Initial data had been cleared off from sequences with a grade lower than Q < 20 via FASTQ filter quality (http://hannonlab.cshl.edu/fastx_toolkit). Since RNA sequencing data contained rRNA sequences it was necessary to conduct the removal of rRNA sequences from the raw data using riboPicker tool. The resulting data set was assembled with Trinity (version 20130814) in accordance with the guidance provided by the developers, and the default settings. To identify retroelements in assembled sequences RepeatMasker program was used [7]. The program uses Repbase the repetitive elements library [8].

3. Results

3.1. De novo assembly, retroelements identification and classification

After quality filtration and rRNA cleaning a 110,746 high quality reads were assembled to 1558 contigs. Length of contigs varied from 201 to 11,902 bp. Average length was 421 bp and N50 was 442 bp. In result of 1558 contigs analysis by RepeatMasker, 70 mobile genetic elements were identified (Table 1).

Table 1.

Results of retroelements identification.

Code	Name of element	Class	Gene identified in contig	E value	Sequence of contig, 5′–3′
c1001_g1_i1	Gypsy-32_PAb-I	LTR/Gypsy	Reverse transcriptase	4E − 05	GAATATGATATCTTATTTCAAGAACCTGAAGGTCTGCCACCAAAAGGGAAATTGTACATGATA TTAATTTGCAGCAAGATGTTCAATTGCCTAACATCTGAATGTACAGGTTATCCACTTTAGAGAA TGCAGAAATCAAGAAGCAGGTACAGGAGCTGCTCGAGAAAGGTTCATAAGACCAAGCACATC ACCATGCGGATCTCCAATAGTGTTGGTGAAAAGAAGG ATGGTTCATGGAGGATGTGCATTGATTAC
c1210_g1_i1	Gypsy-24_PAb-I	LTR/Gypsy	Reverse transcriptase	3E − 07	ACCACCGGACCGGGGTTTGAGCACACCATTGAGCTTCAGCAAGGCATACAGGCAGTGATTAC TACCCCCTATAGGCATCCCAAGGCCTATCGAGATGAGATTGAGCGGGCCATTCAGGAGTTGTT GGCTCTTGGCACATTCGTTCGAGCACGAGTCCTTTTGCTTCTTTCGTGATGTTGGTGAAGAAGA AGGACAACACATTGAGGATGTGCATTGACTACAGGCCCT
c123_g1_i1	IFG-7a_PTa-I	LTR/Gypsy	RNaseH	2E − 46	CAACAATATTGAAGAAAGATGCATTTTTTACTCTAGAAACAACTAAGGCCTTTGAACATCTTA AAGAGACAATGTGCAAAGCTCCGGTCTTAGCTACACCAGACTTCACAAAACCTTTATTGTGGA ATGTGATGCTTCAGGAAATGGAATTGGTGTTGTTTTAATGCAAGATGAAAGACCCATTGCTTT TGAAAGTCGTCCAATCAAGGGAAAGTTTTTAAGCAAAGCTATTTATGAGAAGGAAATGTTGG CAATACTACATGCATTTAAGAAATGGCGACACTACCTAATGGGAAGACACTTCAAGGTAAAA ACGGATCATGATAGCCTTAAATACTTTTAGAAACAAAGTTATTATCCATCTCGAAG
c1288_g1_i1	Gypsy-81_PAb-I	LTR/Gypsy	RNaseH	3E − 16	TAAAGAATTGTATGCATTAGTACAGAGTGTGAAAAAGTGGAAACATTACTTAATGGGCAAAG AGACAGTAATACATACTGATCATCAACCACTTCAATATCTACACTCCCAAACTAAGTTGCAGCA ATCAAGACACTATAGATGGATGGGTTTCTACAACAGTTTCATTTAGTCATCAGATATAAAAAG GGCATACATAACAAAGTTGCAGACATGTTATCTAGACCATTATAAATGCATCTATATACTTAA GCATAATTTGTACTACATGAAAGCTACAT
c1319_g1_i1	Gypsy-71_PAb-I	LTR/Gypsy	Integrase	3E − 23	CCATATTCAAGTCACCCAAGTTATCAAAAGACGCTGACAGCAGTGAAGAAGTTTTATTATTGG CCGAATTTGAAAAGGATGTAGCAAAATTTGTGCTAGGTGTTTGGATTGTCAGCAGGTGAAGG CGGAGTGTAAGCGTCCAGGTGGATTGCTACAGCGAATTGCGATTCTAGAGTGGAAATGGGAG GTCATTTCCATGGACTTTATCATAGGTTTGTCGAGGACAATGAGACAACATGATTCCATCATG GTTGTTATGGACAGGTTGACAAAAATTG
c1441_g1_i1	Gypsy-81_PAb-I	LTR/Gypsy	Reverse transcriptase	3E − 11	TGTTTTTAGACCATTCATTGATGATTTTGTGATAGTCTATTTAGACGATATTCTTGTTTTCAAGA GAACATGGGATGAACATGTAAAGCATGTAAAGCAGATTTCAGATGTTTTGAAAAGAGAAA
c367_g1_i1	Gypsy-20_PAb-I	LTR/Gypsy	RNaseH	1E − 06	CAGGATACTATAAAAGATTCATAAAGAATTACGCACACGAGACTATTCCTTTAACGAATTTAC TAAAGAAAAATTCATTTCAATGGGACAATAAAGCAGATAAATGCTATTTAAAATCCTTAAAAG AGATAATTTCATCTACTCTGGTTTTGGCAACCCCTGATTTCTCCAAACCTTTTGTGGTAGAGTG TGATGCCTCAGGGTTTGGGATTGGTGTAGTGCTAATGCAAGATGATCACCCCTAGCTTACGAA AGTCGAAAACTA
c390_g1_i1	IFG-7a_PTa-I	LTR/Gypsy	Integrase	3E − 87	CAATGTTGGAGGAGATTCAATGGATTTATCAGAGGTTTACCCAAGTCCAAAGAAAGAGTGTT ATCAATGGTGGTAGTTGACAAACTTACCACGTATGCACATTTTGTGCATTATCACATCATTTAA AGCCAGTACAGTTTCTACTGCATTTATGGAAACAATTCAAAGCTACATGGAAACCCAAAGATT ATTGTAAGTGACAGAGATCCCATTTTCACTGGAAATTTTTGGACAGAATTATTTTCTTGTCTTG GTACTCAGTTAGCTCATAGCTCATCTTATCATCCTAATCTGATGGGCAAACTGAGATAGTAAA CAAATGTTTGGAAGGATATCTTCGTTGCTTTGTATCTGATAAACAGACACAATGGGTCAAATG GTTGCCTCTAGCTGAATGGTGGTATAACACTTCCTTCCATACCGTAGCAAAATGACCCATTTAT GGCACTTTATGGATATCTTCCACCATCCATCACATCATATTTAAGAGAAAATTCTAAGGTTCAA GCAGTGGAAAATCACATCAAGCATCAACAAGAAGTTCTCCAACTCTTAAAGAATAACCTCGTG TTGGCGCAGAATAGAATGAAACAACAGGCAGATCAACATCGCAACGAAAGAAGTTTTGATGT AGGTGACTGGGTATTCCTACGGCTACAACCATATAAACAAATGTCCCTCAAGCAAGCTAAGAA GGATAATAAATTATCACCAAAGTACTATGGTCCTTACAAGTATTGCAAAGATTAGTACTATGG CATACAA
c422_g1_i1	Gypsy-58_PAb-I	LTR/Gypsy	Reverse transcriptase	4E − 14	TGCACCCGCAACATTTCAGAGAGTAGTATTAACAATTTTGCTAATCTGGTCCACGAATGTGTTG AGGTATATATGGATGATTTTCAGTATATGGTGATTCCTTTGACAATTCTTTGCAAAATCTTGAA AAAAATTACAACGATGTATAGAAACCAACTTGTCGTTAAGCAGTGAAAAATGTTATATGATGA TGAATGAGGGAATAGTCTTAGGACATCATATTTCTCCTGAGGGAATCAAGGTAGACC
c434_g1_i1	PGGYPSYX1	LTR/Gypsy	Reverse transcriptase	1E − 08	ACATATTGATGGCCTTCTTGACCAACTCAAGGGGCCACATACTTAAACAAGATTGATTGAAGT TTGGCTATCACCAGGTTCCAATAGAACCCACATATGTATGGAAGATCGCCGTGAAATCTAAGA ATGACCTTTTTAGGTGGTTGGTCATGCCTTTGGGTTGACAAATGCCCCTGCAACTTTTATGAGG CTGATGGATGACATCTTGCGGTCCTTCAC
c530_g1_i1	Gypsy-69_PAb-I	LTR/Gypsy	Protease	2E − 11	GACAAGTTAAGATTAGTGAAAAAGTACACCCTACTCCTTACAAAGTGTCATGGCTGCAAAAA GGACATCAGCTTATTGTGACAGAAACAATGCAAGGTAGAAATCTAGATTAGTACTTATAGGG ATGTGGTATTATGTGATGTAATGCCAATGGATGTATGCCATGTATTGCTAGGAAGACCTTGAC AGTTTGATCAGAAA
c6_g1_i1	IFG-7a_PTa-I	LTR/Gypsy	Protease	2E − 46	ATGAATCAGACCATATCTTGTAAAGCATTGGCAAGAGTTACCACTCCTCAAACTCTCAAGATA GGACATATCAAGAAGAAAAAGGTAAGAGTGTTGATTGATTCGGGCAATAACCATAATTTTAT TGATTGTAAGATAGCCAAGGAATTGAATTGCTTCCTATATCCAGCACCAGAGTGTCAAGTGAT GATTGCAAATGGAGGAACAATAAATTGCTCTGGAAAGTGCCATAATATTAAGCTATCCATGG GAGAATATGTATTGACTAGCCCAATGCTTTCCATTCCAATGGGAGGTGCTGATGTTGTACTAG GAGTCCAATGGCTACAATCCTTGGGTACAATAGCTTTTAATTTTCAAGAACTTTTCATGAAGTT TTTCTGTGGAAGGAAAGGAATTTGAATTAAGGGGTATTGCAGGGAAACCAGGAAAGATAAT CAGTCTAATGGCATGACAAAGCTTCTAAAAAAGGAGCAAAGGGGTGTAATTGCACAATTATG TTCGCTAGATGTTTCCACATTAGAATCATCTATTTCTCCAGATCTCCAAAAAGTCCTGGACAAT CATTCCAAGGTATTTGAGACTCCCAAATGTCTCCCACCTATGCGTGATCATGATCATGCTATTC ATCTGATTCCAGGAAGTGTTCCTCCAACATCAGGCCGTACAGATATCCCTATGTCCAAAAAGT GAAATTGAACGTATGGTTGCAGAAATGCTAGAGGCTGGTATAATTCAACCGAGTCAAAGTTC TTTCTCTGCTCCAG
c611_g1_i1	IFG-7a_PTa-I	LTR/Gypsy	RNaseH	9E − 33	AGAAGAAAGACCCATTGCTTTCGAAAGTCGTCCAATCAAAGGAAAATATTTACACAAAGCTA TTTATGAGAAGGAAATGTTGGCAATACTACATGCACTTAAGAAATGGCGACCCTACCTAATGG GAAGACACTTCAAGGTAAAAACAGATCATGATAGCCTTAAAATACTTTTTAGAAACAAAGAT TATCCTCTGAAGAGC
c896_g1_i1	Gypsy-15_PAb-I	LTR/Gypsy	RNaseH	4E − 08	ATGGTCGCTTTAAAGATCTGGAGACACTATTTGGTGGGACGAAAGTTTACACTTAAAAGCGAC CATCAAGTCTACAATATTTGTTCACCCAAAGAGACTTAAATGCCAGGCAAAGGCGATGGAGT GATTCCTAAGTGAATATGACTTCGGAATATCATATATTAAGG
c897_g1_i1	Gypsy-78_PAb-I	LTR/Gypsy	RNaseH	3E − 12	AACTGCCCTACCTACGATAAGGAGCTCTATGCCACGGTGCAAGCTGGGAGGAAGTGGAAGCA CTATCTGATGGGAAAGGAGACAATAATCCACACAGATCACCAGCCGTTACAGTAAATGCAGG CCTAGAATAAGCTACAACTGACCAAGCAATACAAGTGGATGGGTTTTACTACAGTTTCATTTG GTGATCAAGTATAAGAAAGGCATCACAAACAAGTTGGCCGATATGCTTTCA
c954_g1_i1	Gypsy-6_PAb-I	LTR/Gypsy	Reverse transcriptase	6E − 29	GGTGACGGAGCAAGACATCCCCAAGACAACTTTCAGATGACATTATGGGCATTTCGAGTTCCT GGTCATGCCTTTTGGGTTGAACAATGCACCGGCTCCTTTCCAGTCGTGCATGAACCACGTGTT CAGAGGTTAGCTGAGGAGGTTCGTACTAGTATTCTTTGATGGAATTTTGATCTACAATAGGAC ATGGGAGGAGCACCCAA
c1010_g1_i1	Copia-22_PAb-I	LTR/Copia	Integrase	0.088	TCATTTTAGAATTTTGGAAGTCCCGTATACTTTCATGTGACCAAACAAGAAAGAAGCAAACTG GGTGCATCTAGAAAGAAGGAATCTTTGAGGCTATAGCGAAATTCTAAGGGCTATAGAATTTA TGTGGATGGTCAAAGGGAAGTTGAGAGAAGTCATGATGTCACCTTTGATAAAGATATGGCTC TTAGCAAGGTTGACAACCTTCC
c1063_g1_i1	Copia-17_PTa-I	LTR/Copia	Reverse transcriptase	5E − 06	TTCATCAAGAATGACACAGATCCCGACCTCTACTACTTGATGGTAGAGGATGAGACACTCATT TAGTTTTATATATGGATGACCTCTTCTTGACAGGGTCATCAAGTCTTATAGATGACTACAAGAG GAACTTTAAAACAAAGTTTGACATGAAGGATTTGGGTTGATGCACTGTTTCCTAGGCTTGGAA GTGTGGCAGATATATGGGGAGATCTTCCTTGGTCAAGGGAGATATGCTA
c1088_g1_i1	Copia-37_RC-I	LTR/Copia	Integrase	8E − 12	TATTTCATGTTGATAATTGATGATTTCAGCAAGATGATATGGGTTGTTTTCTTAGAGAGAAATC TAGAGCCTTTGAAGTTCAAATAATTCAAATTTATGGCTGAAATGAAATTGATTGCAAGATCAA GAGCATAAAATCTGATAATGGAAATGAGTTCACTTCAAAAGAGTTTGATGAATTTTGCAAGAA GCATGGCATCAAAAGGTTGTTCACT
c1105_g1_i1	Copia-13_PAb-I	LTR/Copia	Integrase	3E − 12	ATATTGAGGCCGATAATGGGACCGAATATGAGTCAAATGAATTCAGAGACTATTTAGAGAAG CTGGAATTAAGAGGGAGACTACTACTGCATATACTCTTGGACAAAATGGTGTCGTCGAAAGG AAGAATCATACTATCGTAGAAGCCACCCGTGCTATGCTTCGTGATCAAGGTCTTTCGAAGTTCT TATGGGGAGA
c1161_g1_i1	Copia-20_PAb-I	LTR/Copia	Integrase	5E − 16	TCAAGGAGTTCAAGGCTCTGGTGGAGAATCTGACTGGGAAGAAAATAAAAGTTTTGCGCTCA GAATAATTGGTGGAGAGTATGTCGATAAGGACTTCACTGATTTTTGCGCTAAGGA GGGCAATTAGAAGAGAAGTGGACAACTCCCTACAATTCAGAGCAGAATGGAGTAGCAGAAA AGAAAGAAACAAGACTATTAGTAGAAGCAGCTAGGGCCATGATGTATGATCAGGATATGCCA AAATTCCTGTGGGCAGAAGCATGCAGCACGGCAGTGTATGTCCAGAACAAGACTCCTCAT
c1211_g1_i1	Copia-28_PAb-I	LTR/Copia	Reverse transcriptase	2E − 11	GAATTTTACATGAAGGATTTGGGGTTGATGCACTATTTCCTAGGATTGGAAGTGTGGAAGAA GGATGGGGAGATCTTCCTTGGGCAAGGAAGATACGCTACAAATATTCTGAAGAGGTTCAGAA TGTAGGATTGCAGACCCATGTCTACGCCCATGATTAC
c1221_g1_i1	Copia-7_PAb-I	LTR/Copia	RNaseH	2E − 49	GGATATGTAGATGCTGACTATGCAGGTGATTTGGACAAAAGCAGATCTACTACAGGTTACGT CTTTACTCTTGCAGGTGGAGCAATTAGTTGGATGTCAAAGCTTCAAGACACGGTTGCATTGTC CACTACCGAAGCTGAATATATAGCTGCTTCAGATGCCAGTAAAGAAGCAATCTGGTTAAAGG GTCTGCTTGATGAGATTGGACGGACATAGAAGAAAGTGAATGTACTTTGTGACAGTCAAAGT GCTATTCACTTGGCCACAAACCCTGCCTATCACAGTAGAACCAAGCACATTGATGTGAGATAT CATTTT
c1222_g1_i1	Copia-27_PAb-I	LTR/Copia	Integrase	5E − 16	CCTTATAATCCTCTGCAAATGCAGTAGCTGAGAGGAAAATAGAACCCTTGTTGAAGCCTCCAA AGCAATGATGTTTGACCAAGACCTTCCTATCTCTCTTTGGGCCGAAGCTACCAGGACAGTGGT TTACATTCAAACCGTAGCCTCATTCCATTCTCAAGGATAAAACACCTGAAGAAGCTTTCACTGG AGTCAAGCCTGATGTAAGCCACTTTAGAGTCTTTGGTTGCCCAGCTTACATTCATGTTCCCAAG GACAAGAGGTCCAAACT
c1223_g1_i1	Copia-28_PAb-I	LTR/Copia	Reverse transcriptase	5E − 13	GGATCGATAGCTACTTGATGAAGTTGGGATTCACTAGGAGTGAAGCCGATCCTAACCTTTACT TTAAGGTTGAAGATGACAAGCCTCTCATACTGGTGTTGTATGTGGATGACCTCTTTCTAACAG GTGCAGACCCTCTCATTCACAAATGTAAGAGGGAGTTGGCTTCTGAATTTGAAATGAAGGACC AAGGACTTGAAGTGTGGCAGAAGCCAAGGGAAATTTTCCTATCTCAAGGAAAATAT
c1242_g1_i1	Copia-27_PAb-I	LTR/Copia	Integrase	4E − 10	GGAAAAAGAATCAAGACGTGAGGACCAACAATGGAACCGAACATGAATCTAATGAATTCAAT GACTTTTGTAGAGAGGCAAGCATTAAGAGGGAGACACCCATTTTGTATACTCCAAAGCAAAAT GGTGTTGTTGAAAAAAGAATCGAACTATTATGGAAGCCACTCGTGCCATGCTCTATGATCAAG GTCTACTGAAATTCTTGTGGGAGAAG
c1252_g1_i1	Copia-1_PAb-I	LTR/Copia	Reverse transcriptase	3E − 06	TGTTATATGAGGATGACCTCTTCATAACAGGTGCAGACCCTCTCATTCACAAATGTAAGAGGG AGTTGGCTTCTGAATTTGAAATGAAGGACCTAGGACTTGAAGTGTGGCAGAAGCAAGGGAAA TTTTCCT
c1260_g1_i1	Copia-4_PAb-I	LTR/Copia	Integrase	2E − 09	AATAGGTGTCCATCTCATGCTCTCAAAATAAAGACTCCCTATGAAATTTGGTATGGCCACATTC CTTTGGTAAGCATCTCAAGGTTTTGGTTCCACCTGTTATGCCTTGGTTCCTAAGGAACAAAGAA ATAACTTGGTGCAAGGAGTTGAAAATGTATCTTCTTGGGATACTCAAATACCTCCAAAGCATA TCGTCTCTGTGATGAAGTAATAAGAAGCTTATAATATCTAGAGATGTGATATTTTT
c1262_g1_i1	Copia-28_PAb-I	LTR/Copia	GAG	1E − 06	AAGATAAGATGCTATGGATGTCATGAACTTGGGCACTATAGAAGAGATTGTCCTAATCATAGT AAGGACAAGGGGAATAGGGAAGAAGCCCACATTACTGAAGAAGTGAAAGAACCTGAGTCAA AGAAGCTTAAAAATGAAGAAGTAAAAGATCTC
c1264_g1_i1	Copia-15_PAb-I	LTR/Copia	Integrase	5E − 27	TCAGCAGTTGGGGGTATGCAGCGCCTGTCAAGCGGGAAAGCAACATCGGTCTTCATTCAAAA ATGGAGAATCTTGGTGCGCATCTAAGGTACTTCAGTTACTTCATGCTGATATTTGTGGTCCTAT GAATACAGCTTCTATCACTGCTTGCAAATATTTTTTACTTATTGTAGATGATTTCAGTAGAAAG ATGTGGGTGTATTTTTAAAAATAAATCTGATGCTCTTAGTACCTTTCAGAAGTTTAAAACATTA GTTGAAAACGAATCTGGTTGTAATATCATGACCCTTAGGACCGACAATGGGGGGAATTTGTTC CTCAGCTTTGCCAACTTCTGTGATATTCATGGCATCAAACGTCAAT
c1371_g1_i1	Copia-27_PAb-I	LTR/Copia	Reverse transcriptase	2E − 05	TTCGAGATGAAAGACCTAGGACTGATGCACTATTTCCTAGGCCTGGAGGTCTGGCAGAGACCT GGAGAGATTTTCCTTCTCAAGGAAAGTATATTGTGAAGCTTCTGGAAAGATTTGGGATGGTGG ACTGTAAGTCCGTGTCGACACCAATGGAACTCAACTTTAAGAAGTTGAGTG
c1384_g1_i1	Copia-25_PAb-I	LTR/Copia	Reverse transcriptase	2E − 06	TTTCTTCTTCAGATGATGAAAGTGAGGAGGATGATAATCCTCCCCCACCTTCTCAGGATCCTCA ACTTCCAAGATGGGTCCGTGCTACTCGGGATGCAGCAGGTGATCTTGCCGGTAATCCTACAGA TCAGCGACGTACACGTTCTCAGTTTGAAAGAGCCTCTTCTTTACTGGCTCAAGCTCCAATAAAT CATGATCCTGACACTTTTGCAGAAGCTTCAGGCCATCCACATTGGGAAGCAGCTATGAATGAA GAATATCATTCATTGATGACAAATGATACATGGGAT
c1404_g1_i1	Copia49-PTR_I	LTR/Copia	RNaseH	2E − 22	TTACATATGAAGCAAGTCGGTCCTATGAAGTTATACTGTGATAACAATGCAGCATGTGATACT GCTCATAATCCAGTTCAACATGATCGAACTAAGCATGTTGAGGTTGATAGGCATTTTATCAAG GAGAAACTAGAAGCAAAGTTGATTGTAGTTCCTCATGTTCGATCTCAAGAATAGCTTGGTGAT GTGCTGACCAAAGCAGTTGTCAAACCAAGCATT
c1452_g1_i1	Copia-20_PAb-I	LTR/Copia	Integrase	1E − 13	AGACAATAGAGGTGAGTACACAGATAGTGACTTCACTAGTTTTGTGCACAGGAAGGCATCAG GAGGATTGGACAATTCCATACAATCCACAACAAAATGGGGTAGCAGAGTGGAAGAACAAGTT TATAATTGGGGCTGCAAAGGCAATGTTATATGACCGGGATTTTCCCAAGTTTCTGTGGGCAAA GAAATGTAACACAGCTATGTATATACAAAACAGGGTTCCT
c1457_g1_i1	Copia-28_PAb-I	LTR/Copia	Integrase	2E − 24	TAAATGAAGAAGGATGAAACATTCCAATGGTTCCGCTCTTTCAAAGCCTTGGTTGAAAATCAA ACAGGGAAGAAGATCAAAATGTTAAGGATTGATAATGGAACTGAATATGAATCAAATGAGTT CAATGACTATTGTAGAGAAGCTGGCATTAAGAGGGAGACTACTACCGCATATACTCTCGAACA AAATGGAGTTGCTGAAAGAAAGAATCGTTCGACTATAGAA
c1458_g1_i1	Copia-28_PAb-I	LTR/Copia	Integrase	4E − 21	CATGAAGGAGTATGTAAGGGATGTGCATTGGATAAGAATACCAAGAGACCATTTGGAAGCAG TGTTTCATGGTCAAAAGAAATCTTGGATCTCATTCACTATGATGTATGTGGCCCTATGACTCCT AAATCACTTGGAGGTCATCTATATTATGTCACATTTGTCGATGATCATTCAAGAAAGACCTAGT TTAACTTAATGAAAACCAAGGACGAAGTATTTACAAAATTTCAAGAATTCAAAGTTGAAG
c169_g3_i2	Copia-25_PAb-I	LTR/Copia	Protease	4E − 06	TTCTCATGAGTGGCTCATTGATTCTGGAGCTTCTTATCACAATAGGCCAAAACAAAGCCATGTT TTCTTCTTTAAATGATTGTAACACCAAAATATATATGTTGGTATGATAGATCTCTTAATGTTGTA GGGACTGGAACTGTTCATCTAGACAATGGTCAGTTCAATGATGTATTATGTGTTCCAAACCTAT CCTGCAACCTTCTATCTGACTATCAGATAACTCATTCAGGTGAAGGTAAAATCGTTGAATTTTC ACCTCACGATGTTGTAATTAAGGACCTAA
c217_g1_i1	Copia-25_PAb-I	LTR/Copia	RNaseH	0.099	ATACTTCGTTATGTTCGAGGTACAATTCAGTTTACAGTGCAGAAGCATCTCCTCTATTGGTTGG TTTCACTAATTCTGATTGCGTCGGTGACCCTGATGATTG
c217_g1_i2	Copia-25_PAb-I	LTR/Copia	RNaseH	3E − 30	GGAAGCCTACTGCAGGTTATGTGTTCACTCTTGGTTCAGGACCTATTACATGGGCTTGCAAGA AACAAAGTGCCATTTCTCTTTCTTCAGCAGAAGCAGAGTATCCTGGTGCCGTAGAAGCTAGTA AGGAAGCCTTGTGGCTTCGTCAGATCCTATCAGAGTTTGGCTTTGAGCAGCAGCATCCGACTA CACTTTGGTGTGATAATCAAAGTGCCATTCAGCTATGCAAAGATCCAGTCCAGCATCAGCGCA GCAAACACATTGAACT
c346_g1_i1	Copia-28_PAb-I	LTR/Copia	Reverse transcriptase	0.002	CCTGAAAACAAAAAGAGACCTAATTGGTTGAAGTCAACTCTTGTAGATGCAGAAGGGCATGG AGCAGCCAAAGGAACACTCAAGGAAAGTAAGAAGCCCAAAAGATATTCAAGGTATGCAGCTT ATATGACAAAGTTAATAGAAGCAGAACCATCCACCTTTGAAAAAGTTGTCAAACATCAAGAAT GGAAAGATGCCATGAATGAAGAATATCAATCAATAATGAAAAATGGAGTTTGGGA
c53_g1_i1	Copia-1_PAb-I	LTR/Copia	RNaseH	8E − 19	TGCAACAATCATAGTTGCATCAAAGCTCTCTGAGAATCCAGTGTTTCATGATAGGTCGAAGCA TATTGATATTCGGCGTCACTTTGTCAGAGACTGTGTCCAACGAGGAGTTGTACAGTTGAGCTA CACTCCTACAGGAGAACATGCGGTAGACATCCTTACCAAGGCCCTTGGAAGAACAAAGTTCAG ATATTTCAGGGAGAAGATGGGGATGGTAAAAATCCATTTCAGTAGCAGAAATGGA
c533_g1_i1	Copia-30_ECa-I	LTR/Copia	Reverse transcriptase	3E − 12	AAGTATGTAGATTAGTTAAAGCACTCTATGAATTGAAACAAGCTCCTCGAGCTTGGTACATGA AAATTGATCAGTACCTAATAGATCATGGCTTTCAGCGAAGCCCATCTGA
c543_g1_i1	RT_GB	LTR/Copia	Reverse transcriptase	2E − 08	CATTTTCAATGGCTTCATACAGGAGGAGGTGTACATTGAGCAGCCACAGAGCTTTGAGGTGCA TGGAAGGAGTCCCATGTGTGCAGACTGAAGAAGGCCCTTTATGGCCTGAAGCAAGCTCCCAG AGTTGGTACTCCAGGATAGATACATACTTGCAGGGGATGGTTTCACAAAGAGTGAGGCAGAT CCGAACCTTTACCTTATTGTGATAGG
c569_g1_i1	Copia-17_PTa-I	LTR/Copia	Integrase	2E − 05	GGACTGCCATTATTTCTTGGGGCAGAGGCATGCCACAATGTAGTCTTTCAACAGAAACAAGAG TCCACATAAGGTGCTTGGACGAGTTACACCAAAGGAGGTATTCACCGACAAGAAGCCAAATA TTTCTCACTTTTGGATTTTGGCAGTTTATTTTACTACCACGTGCCTTTAGAGAGTTGGGGGAAG CTAGAGCCTACAGTAGAAAAAGGCATTTTCATGTGCTACAATGAGACATCCAAGCATATAGG GTGTAC
c575_g1_i1	Copia-27_PAb-I	LTR/Copia	Reverse transcriptase	3E − 06	AATTATGTATGGGAAGTGGTTCCAAGACCCCAATGTAAATCTGTTGTGTCTTCTAAATGGTTG TATAAATTAAACATGGTGTTGATGGCAGTATTGAAAATATAAAGCTAGATTTGTGGCCAGAAG GTTCTCTCAAAAGAGGGAATAGACTATGATGAAATCTCTGCCCTATTGCATGTTATACAACCA TCTGATCTAT
c591_g1_i1	Copia-12_PAb-I	LTR/Copia	Integrase	8E − 17	TTTGACCGAGGGTCTTCCAAAGTTTCTGTGGGGAGAAGCTGCAAATACTGCTGTGTACATTCA AAACCGATGCCCTCATTCCGCTTTGGACTCCAAAACTCCCGAAGAGGTTTTCTCTGGTAAGAA ACCTAATGTCTTCACATTTTAGAATTTTTGGATGTCCTGTCTATTTTCATGTGCCGAAAGAAAAG AGAAGTAAGCTGGATGCTACTGGGAAGAAAGGAATGTTTGTGGGCTACAGTGAGACTTCTAA GCATATAGAGTCTATGTACCTGGTCAAAGGGAAGTAGAGATAAGCCATGATGTCACTTTTGAC GAAGATGCTTCCCTGAAGAAA
c600_g1_i1	Copia-25_PAb-I	LTR/Copia	RNaseH	2E − 13	TTGCAATCCAAGAGGTATTTCCTTTCCCAGTCCAAGTATGCTTGTGATATTCTTCGTCATTTTCA CATGGAAGACTGTAAGCCAGCCCCTTCTCCCTTTCAGTCTGGAGTCAAACTTTCAGTCTCTTGT ACTTCTCCTGAAGTTGATGCTACCTTATACCGTCAACTTGTAGGAAAACTTTTGTATCTAACCC ATACTCGTCCTGACCTTTCCTTTGTTGTTGGCCTTGTTGCTCGTTTTATGCAAAACCCCCGTGAA AGTCATTGGAAAGCAGCTAAAAGAATACTTCGTTATGTTCGAGGTACAGTACAGTTTGGGATT CATTACAGTGCCAAAGCAGCTCCTCTGTTAGTTGGTTTCACTGATTCTGATTGGGTTGGTGACC CTGATGATCAAAGTCTACAACAAGTTATGTCTTCACTCTTGGTTTTTGGACCTATTACATGGGC TTGCAGGAAACAAAGTTGTCATTTCTCTTTCTTCAGCAAACCAAATGTATCGTGGCACCATTGA AGTTAGTAAGGAAGACCTGTGGCTTCGTCAGACCTATCAGAGTTGGTTTTAGCAGCA
c616_g1_i1	Copia-13_PAb-I	LTR/Copia	Reverse transcriptase	9E − 44	TGATGGGAGTGCTGAAAGTTTAAGGCAAGATTTGTTGCCCGTGGCTTCTCTCAAAGGAAGGA ATTGACTATGACGATATATTTGCACCTGTGGCTCGATATACCACCATCCGATCCATCATAACCC TTGCTTCTACGCAAGGATGGAGTCTTCATCAGATGGATGTCAAGACCGCTTTTCTGCATGGTGC AATAAAGGAAGAGGTGTATGTAGAACAACCTCTGGGATTTGAAGTTCAAGATCGAGACACTT ATGTCTGCAGGTTGAAGAAAGCCCTCTATGGGTTAAAGCAAGCACCCAGAGCTTGGTATGAA AGGATGGATAGTTACTTGATGAAGCTGGGCTTCACTCGAAGCAATGCTGATCCAAACCTTTAC TTTAA
c682_g1_i1	Copia-17_PTa-I	LTR/Copia	GAG	5E − 06	AGGGAAGAATGTTGACAAGTCTAAAGTGAGATGCTTTAATTGTCACGAGATGGGACATTATG TGACTAATTTCCCATCGAAGAATTCCAAGAAGGGATCCTCGAAAGGATCTTAAGGTGAGGCAT TAGCTCTTAGTTCGAAATGGACTTTACCCTCATCGCATGCATGGTGTCGTCGATGGTGAATTGT GTTTTGTATCTTGACAGTGGAGCCTCATTCCACATGATTGGTG
c726_g1_i1	Copia-28_PAb-I	LTR/Copia	Reverse transcriptase/RNaseH	0.058/0.097	GAATTTGACATGAAGGACCTTGGTTGATGCATTACTATTTGGGACTGGTAGTTTGGCAAGAAC CTAATGAAGTCTACTTAGCTCAAGGAAGTATGTGTTCGAGATATTGAAGAAGTTCGACATGAT GGACTGTAAACCAATGACCACTCCAATGATTACTAATGTGAAGAAACTAAGAAGTTCTGAATC AAGCCCTATGGATCCTTCCAAATATAGAAAACTCATTGGTTCACTAATGTATTTAGTGAATACT AGGCC
c755_g1_i1	Copia-15_PAb-I	LTR/Copia	Integrase	2E − 12	TACATTCCACAAATAGAATGGAGTGGTTGAAAGTTGGAACTGCACTAGCAGTAAGATGGCCA GTTGTAATGTTATAGAAAAGTGTGTTCCAAACAAGTTTCGGGCTAATTCAGTGTTCACAACAC TACACATGCTGTATAGATCTCCAATGATGGCAGTGATAGAAAAGACTTGAAAGGAATTGTGGT CTAGAAGAAAGTCCAAAGTCAATCATCTTAAAGTCTTTGGTTCTATTGCTACATTCG
c820_g1_i1	Copia-28_PAb-I	LTR/Copia	Integrase	0.023	TATGTCCATGTGCCAAAGGAGAAGCGAAAGAAGTTGGAATCGACAAGCATCAAGTATATTTG TTGGATATAGTCTTTCCTCAAAAGCTTATAGAATCTACATAAAGGAGGGAAGATACATTGAAG TAAGCAGGGATGTCATATTTGATGAGAATCAAGCTTACAAGAAAATCAAAGGATATTCCTAAT GATTCCGATGACGAAGA
c832_g1_i1	Copia-20_PAb-I	LTR/Copia	RNaseH	0.013	GATCCCACTATGTATAGGAAGTTTATTGGATCCTTGCTGTACCTGGTTAACACCGAGGCAGAT ATTTCCTTTGTAGTGAGCACCCTAAGCTAGTTTATGTTGAGCCAAGGCATGGACATTGGTTGC AGTTAAACATGTATTGAGGTACCTGCATGGTACAATTGGATATGGTCTTAAATATGTCTAAGT GGTGAAGTGAGGTTATAGGGATATGCCAATTCTGATTGGGTTGGGATCATGGT
c86_g1_i1	Copia-20_PAb-I	LTR/Copia	Integrase	9E − 05	TACATGACAATGACAACTTGTGTGAGCTATGACACAGGAGGTTGGGACACCTACACTACATG GCATTATAAATCTCGAGGGAGATTGCCATTGGTCTCCCAAATTTCAATATTAAGTAATAGGGC ATGTGTAGAGGTTGTGCACTTTACAAGAGTGCCAAAGCTCCTTTTCGAGCGACGAGAGTATGT CCA
c905_g1_i1	Copia-28_PAb-I	LTR/Copia	Reverse transcriptase	9E − 06	GATCAGAACCTTTATTTAAGGTTAAAATGATAAATCTCTCATATTGGTACTTTATATGGACGAC CTCTTTTGACAGGTGCAAACCTCTCATTACAATGTAAGAGAGAGTTGGCTTCTAAATTTGAGAT GAATGACCTAACACTGATGCACTACTTCCTAAAGTTGGAGGTCTGGCAAAGCCAAGAAAATTT TCCTATCTCAAAGAAATATGTTGTGAAATATTGGAAAGATTTGGAATGGTGGACTGCAACCCT ATGACTACCCCAATAG
c968_g1_i1	Copia-4_PAb-I	LTR/Copia	Integrase	8E − 27	CTCATTCATTCAGATTTATGCGGTACAATGCATGTTCCTTTTGCAAATGGAAATAAATATATGA TGACATTTATTGATGACTACACCAGAATGTGTTGGGTTTATTTATTGAAGAACAAATCTGATAC TTTTCAAACATTCAAGAACTTTCATACATGAATTGAAAATGATGCACAATCCCATATTGGCTCT ATTCACACTGATAATGGAAAAGAATACACTTCAAATGAATTTGAAA
c97_g1_i1	Copia-4_PAb-I	LTR/Copia	Integrase	6E − 25	TTTCATGCATTGATTGAAAATGATGCTTAATCTCATATTGGTTCTATTCGTACTGATAATGGAA AAGAATACACTTCAAATGAATTTGAAAACTATCTTCGCCAACATGGGATCAAACATCAAACAA TTGTACCTTATAATCCCCAACAGAATGGTGTAGCTGAAAGAATGAATAGGACAATCTTAAATA TGGTACGATCCATGCTCTTCTTCAAAATGTAAAGATAAAGTTTTGGG
c1375_g1_i1	Copia-28_PAb-I	LTR/Copia	RNaseH_Copia	1E − 11	TTGATGTTCTTAGTGAACACCCGTCCGGACATATGTTTTGCAGTGAATACTTTGAGTCAACAGA TGGTTGAGCCTCATCATTTTCACTGGGTTGGTGCCAAGAATCTTTTGAGATATCTTCGGGGCAC GATAAACCATGGGCTGAGATACACTGCCGGGAGTGTGATACTCCGGGGATATACTGATGCCG ATTGGGCTGGCAGTGTGGTGGATCGTAAGAGCACATCTGGATGCTGTTTCAATCTTGGTTTCT GCTTTCGATCTCATGGATGAGCAGGAAGCAGAAG
c1146_g1_i1	Copia-20_PAb-I	LTR/Copia	Integrase	1E − 58	AGTAGTGACAGCAGAGCGACTGGGATACTTGATTTGATTCATTCTGATGTGAGCGGTCGGATG TCTCATGTTTCCTTGAGTGGATATGAGTACTATGTTTTATTCATTGATGATCACTCCAGGAGGA CCTGGATTTTTTTCTTGAAGACCAAGAGTGAGGTCTTCAAGCGGTTTCAGGAGTTCAGAGCTCT TGTGGAGACTCAGACAGGTCGAAAGATCAAGTCCCTGAGGTCGGACAATGGAGGAGAGTACA CCCTTGGAGAGTTTGTTGACTATTGTGCGGAGGCAGGCATTAGGAGGGAGTTTACTGTTCCTT ACAACCCCCAGCAGAATGGGGTTGCGGAGAGGAAGAACAGATCCATCATAGGGCTGCCAAA GCCATGTTACATGATCAGGGGTTGCCATTGTTCTTGTGGGCAGAGGCCTGCAACACAGCTGTT TACTTGCAGAACAGGAGTCCGCATCGTGCCTTGGGGCACATGACTCTGGAGGAGGCTTTCTCT GGGAAGAAGCCTGATCTTGGTCATCTTCATATCTTTGGATGCATTACATACTCCTATATACCCA AGGAGAAGAGGACCAAACTAGAGCCCACCGCAGAGAAGGGTATCTTTGTGGGCTACAGTGA GACCTCAAAGGCCTTTCGGATTTACATTCCTGCACAGAGGAGAGTTGTTGTCAGGCGGGATGT GAAGTTCGAGGAGGACAGGGCCTT
c238_g1_i1	Copia-4_PAb-I	LTR/Copia	Reverse transcriptase/RNaseH	3E − 44/2e − 44	ATGATTGTGAATTGAACTTGTCTACAGATTTTGAACCAACTTCCTTCAAAGAAGCTGCTTCTCA TGATGAATGGAAAGAAGCGATGCAAAGGAGTATGATGCCCTCATAAAGAATGGCACTTGGA AGCTGGTTGATCCTCCATTTGGAACCAAACCAATTGGCTGCAAGTGGGTCTACAAGAACAAAT ACAAAGTTGATGGCTCACTTGACAAGCACAAAGCTAGGCTTGTGGCAAAAGGTTTTGCACAGA AGGAAGGGGTCGATTATGAGGAAACTTTGCCCCACAGCAAAATGGGCCACCATCCGGACACT CTTTGCACTAGCTGCTCAGAACGGTTGGAAAGTCCATCAAATGGATGTAAAAACTGCATTCTT GAATGGAGATCTAAAAGAGAATGTTTTATGTCCCAGCCTGAAGGATTTGCTGTGAAAGGACA TGAACACAAAGTATGCAAACTTGTGAAGTCCTTGTATGGCCTCAAACAAGCACCACGAGCCTG GTATGAAAAACTAACTGAGCATCTTCTGAAACTCAACTTCAAACATTTTGATCTTGATGATGCA ACTTTATTTGTCAAGAAAGTTGGCAAAACAGTTGTATATCTTGTGGTATATGTAGATGATCTTT TAATGACAGGGAACAATGAAAGCTATATTGCATCCATAAAGAAAGAATTAGGAAAATTTTTG AAATGACTGATTTGGGCTATGTTCATTACTATCTTGGCATTGAAGTAACCCAACATCCAAAATC CATATTTCTTTCTCAAAAGAAATACATTGGAGATTTGTTAAACAGATTTGGCATGACAGAGTG CAATCCTCTTTCTACTCCAATGGAACAAAACTTGAAGCTCACATCTATTGAAGGAAAGGAATTT GAGGATGCAACAAAGTATAGACAGCTTGTAGGAAGTCTCATCTACTCACTACTACCAGACCAG ACATTTCATTTGCTGTTGGAATCCTCTCCAGGTTCATGCAAAAGCCTTGTGAGGGACATTGGTC TGCTGCAAAAAGAGTTCTAAGGTACTTGAAGGGAACTCAAGACTTTGGAATCAAGTATACACA GGTGGACGACTTCAGCTTGATTGGATACTCTGATTCAGACTTCGATGGAGACAAAGAAACTGG GGTATCTACTTCAGGATATGCTATGAGTCTTGGATCAGGAGCTGTCTCCTGGAGATCACGCAA ACAATCAGTTCCAGCAGATTCCACAACAGAAGCAGAATACGTGGCAGCAGCTGAAGCAACGA AAGAAATTGTGTGGCTCAGGAAAATCATTGAAGATTGCCAAGGAAAACAAATACAATCAACT CCACTCATGATTGACAACACCTCGGCAATAAAGTTGGCCAAGAACCCAAAGTTCCATGATCGA ACGAAGCACATCAATACAAAATATCATCTGATCCGACATCACGTTGAGGCCAAAACAATCCAT CTCCGCCATTGTTCCACAAACGAGCAAATTGCAGACATCTTCACCAAAGCGCTTGGAAGAGAA AAGCTTGAAAGATTCAGAACGATGCTTGGACTCACCAACATCCCTTCAGATTAAGGGGGGAAT GTTGACACCTAATCCG
c42_g1_i1	Copia-27_PAb-I	LTR/Copia	RNaseH	3E − 40	CTTTGGTTTGGAGGTGTGGCGAGGAGAGGGCATTCTTCCTGGGCAGGGAAGTATATTGTGGA CATCCTTGGCAGATTCCACATGGAGGATTGTAAACCCATGTCGACACCGATGATCACCAACTG GAAGAAGCTTCATGCTTCGGATTCCGAGTTGGTGGATCCCACATTGTACAGGCAGCTGATTGG TTCCTTGATGTATTTGGTCAACACTAGACCAAATATCTGTTTTGCAGTCAACACGATGAGTCAG TTTATGTGTGAGCTAGGAAGGTTCATGGGTGGCTGCAAACACGATTTGCGGTACTTGCAGGGA CAGTGGATTATGGTCTGGACTACAGGCAGGGAGATGGAGTGAGATTGGCAGGGTACACTGA TTCTGATTGGGCAGGTTGTGCTTCTGATAGGAAGAGCACTTCAGGTGTTGTTTGGTTGGTTCA GCAGTAGTGTCATGGTTCAGCCGGAAGCAGCAGTCAGTAGCACTGAGTTCAGCGGAAGCAGA GTATATGGCAACCAGTCTAGCTAGTTGTGAGGCTATCTGGCTTCGCAAGATGTTGTTTGGCTT ATTTGGTCAGCCGTTGAGACCTTCAGTGATTTACTGTGATAATCAGAGTTGCATTAAACTCACG GAGAATCCAGTATTTCATGACAGGTCAAAGCATATCGGGATCAGATATCATTTCATCAGAGAC TATGTTCAGAAGGGAGTTGTGAAGCTTGATTATATTTCCACTGATGAGCTGGTTGCAGATATT CTTACCAAAGCCTTACCACGGGGCAAGCATGTCTACTTCAGGGAGAAGATGGGTGTGGTGAG GAACACCTTCCTCGGTAAGAGGG
c61_g1_i1	Copia-4_PAb-I	LTR/Copia	Integrase	1E − 23	GATCCATGCTTTTCTTCAAAAATGTAAAGATAATGTTTTGGCTGATGCTGTTCTATGTGCTGCA TATATAAAAAATAGATGTCCATCTAATGCTATAAGAAACAAGACTCCATATGAAATGTGGTAT GGACATGTTCCTTCGGTAAAGCATCGCAGGGTCTTTGGTTCCACCTGTTATGCCTTGATACCAA AGGTACATAGAAACAAACTTGGTGCTAGAAGTCATAAGTGTATCTTCCTGGAGTATTCAAACA CATCCAAAGCATACCGCCTTTATGATGAAGTAAATAAAAAGTTTGTTGTATCTAGAGATGTAA TTTTCTTGAATCATCCAAATCTGACAGTGTTGTTGAGCGGCAACTTGATCGCTTGGATAGATTC
c1151_g1_i1	Copia-25_PAb-I	LTR/Copia	Integrase	7E − 35	TTCTTTAAAAAACTCCAAGAGCGTAAGTATATTTAATCAACATTTTAGGCCTTCAAAGCCTTTG TTGAAAAAACAATCTGGACATCAAATTCTTAAGCTAAGAACTGATAATGGTGGAGAATATGTT AAAATGCATTCATCACCTTTTGCACCGAAAATGGAATTCAAATGCAACATACTGTTCCATACAC TCCACAACAAAATGGTGTAGTTGAAAGGAAGAATCGCACCTTAAAGGAAATGGCCTAATTGT ATGCTTCAATCTAAAGGACTTAGTCTTAGTTATTGGGCCGAAGCAATTAATTGTGCAAATTATA TAATCAATCGCACTCCTACTAAGGTTTTAAAGAATATCACTCCAGAAGAAGCTTGGAGTTCCAT TAAACCAGATGTAAGTCACTTTCGTGTTTTTGGAAGTGAAGCATGGGCCCATATTCCAGATGA GAAGCATAAAGCTTTAGAACCTAAGAGTGAGAAATGTACTTTTGTTGGATATTCTGAAGATGT CAAAGGTTATAGACTTATTCCATTTAAGTCCAAAATGTTATCATTAGAAGAGATGTAAAGTTTG TTGAAAATATATCGGCCTGCGAGCCTAGTTCGGCGGATGTGCCACCTCTTCCTATCTCTTCTATC TTTGAGAATATTTCTTCTTCTGATGATGAAAGCGAGGATGATAATCTCCCACCTTCTCAGGATC CTCCTTCAG
c93_g1_i1	Copia-25_PAb-I	LTR/Copia	RNaseH	9E − 47	CCTTGTTCTTTTTCTTGCTGTTTCTTTCAAATTGGAAAGTCTATCAGATGATGTTAAATCTGCCT TTTTGCATGGAGATCTT
c1299_g1_i1	PtCumberland_I	LTR	Reverse transcriptase	1E − 26	AAGGCACTCTATGGTCTTAAAACAGGCTCCAAAGGGCTTGGTATTATCGTCTAGACAAATACC TCCATCAACAAGGTTTTTCGAAAGGATCAGCAGATAGCAATCTATATATAAAAATTGATAATG ATAAATTGCTAATACTTGTCGTATATGTTGACGAGATCATCTTTGGTAGCAATGAAGAAGCCAT GAGTCAAAACTTTGCTTTGGTGATGCAGAAAGAATTTGAAATGTCCTTGCTTAGTGAGCTAAC ATATTTTCTTGGTTTACAAGTCCA
c443_g1_i1	PtCumberland_I	LTR	Integrase	2E − 06	TTTATATTGTTCATTGATGATTTTCCAGAATGTGTTGGATAGTCTTCTAAAGCATAAAGATGAA GCATTTGAAAAGTTCAAAGCCTTCAAAGCTTTGGTTGAAAATGAATTAGATCGCAAATCAAAT GCCTCAGATCTGATCGAGGAGGGAATTTACCTCGGATGAATTCTTTGACTTTTGTGAACAACA TGGAATAAAAGGCAGTTCTCCACTGCAAGGACTCCTCAGCAAAATGGAGTGGTAGAAAGG
c583_g1_i1	PtAppalachian_I	LTR	Protease	0.16	TATGAATCAAGGCCCGTGCTGTTATTATTACATTGGGAAATAAGTTGTTCAGGATACCAGAGG TAGCACCACCTGCCGCCATCTCTTTAATTACTGCAAACAATGCAGTAAGATCATTTCCAAAA
c583_g1_i1_rev	PtAppalachian_I	LTR	Reverse transcriptase	8E − 25	GGGACGTGGAGACTCTGTATTGACTATCGGGCGCTGAACAAGATCACTGTCCGTAATAGGTA CCCGATCCCGCGGATTGATGACCTCCTAGACCAACTAAAGGGGGCGAAATATTTCAGCAAGAT CGATCTGAAGTCAGGATATCACCTGGT
c584_g1_i1	hAT-5_PTr	DNA/hAT	hAT polyprotein	5E − 16	TTTATTTCATTATTTTGTTGTAGATCTTTGGTGGCGAAGCTATGGTGCAAGGGTACCAAATTTG CAAAATTTGGCTATACGAATCTTGAGTCAAACATGTAGCTCTTCAGGGTGTGAGCGCAATTGG AGTGTATTTGAGAAAATACACGCCAAAAAACGCAACAG
c843_g1_i1	SHATAG_MT	DNA/hAT	hAT family C-terminal dimerisation region	8.2e − 05	AATGGTGGGAGCCTTTGGTGGCCAGTGCCTCAATTGCAAAAGTTTGCAATTCGTATTTTGAGT CAAACTTGCAGTGCATCTGGGTGTGAGCGCAATTGGTCTGTCTTTGAGAGGATTCACACAAAG AAGAGAA

A 68 of that were retroelements (Table 2). Most of elements represented by Gypsy (16 contigs) and Copia (48 contigs). In 4 cases retroelements specific to Pinus taeda were identified. It is worth nothing that in two cases DNA-transposons were also identified. In general this data comply previously published where both Gypsy and Copia were shown to be dominant [3].

Table 2.

Classification of identified transposons.

Repeat class	Number of transposons
Transposable element	70
DNA transposon	2
hAT	2
LTR retrotransposon	68
Copia	48
Gypsy	16
PtAppalachian	4

Studies of contigs showed that in most of cases fragments of integrase (24), reverse transcriptase (22) and RNaseH (15) were identified (Table 3). Results of the study may be of interest for coniferous breeding and genetic specialists.

Table 3.

Classification of identified retroelements.

Genes identified in contig	Number of cases
Total number	70
Integrase	24
Reverse transcriptase	22
RNaseH	15
Protease	4
hAT polyprotein	3
GAG	2

Funding

This study was funded by Joint Grant of Russian (RFBR No. 15-54-04004) and Byelorussian (BRFFR No. B15RM-007) Foundations for Fundamental Research.

Conflict of interest

The authors declare that they have no competing interests.