ABSTRACT
Sequences of multidrug-resistant (MDR) Mycobacterium tuberculosis strains are of particular interest to study the molecular mechanisms of drug resistance evolution. Here, we report the draft genome sequences of 77 endemic multidrug-resistant Mycobacterium tuberculosis strains of SIT41 (TUR) spoligotype from Bulgaria. SIT41 spoligotype is dominant (>40%) among the MDR-TB strains in Bulgaria.
ANNOUNCEMENT
The current control of tuberculosis mainly depends on multidrug resistance management. Multidrug-resistant M. tuberculosis (MDR-TB) strains of SIT41 (TUR) spoligotype are endemic to Bulgaria (1–4). SIT41 spoligotype is prevalent (>40%) among patients with MDR tuberculosis and a marker for MDR-TB in Bulgaria.
Seventy-seven MDR-TB strains of SIT41 (TUR) spoligotype were collected in Bulgaria from 2009 to 2019. All strains originated from Bulgarian patients with pulmonary tuberculosis. One isolate per patient was tested. The Bactec MGIT automated mycobacterial detection system (BD, USA) was applied for isolation and drug susceptibility testing at the National Reference Laboratory for Tuberculosis at the National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria. All strains were rifampicin and isoniazid resistant. Genotyping of the isolated MDR-TB strains was performed, applying spoligotyping (5) and 24-loci MIRU-VNTR typing (6).
For DNA isolation, we used a fresh subculture of the isolated MDR-TB strains grown on Löwenstein-Jensen medium for 35 days at 37°C. The DNA was isolated according to the procedure described by van Soolingen (7) including incubations with lysozyme, 10% SDS, proteinase K, 10% cetyltrimethylammonium bromide (CTAB), protein/lipid extraction with phenol/chlorophorm, and DNA precipitation with isopropanol.
Before sequencing, DNAs were quantified by SYBR Green assay (Thermo Fisher Scientific, USA). Quality was validated after agarose gel electrophoresis. The libraries were prepared by using the Nextera XT DNA Library Preparation Kit (Illumina, USA) following the manufacturer’s protocol to achieve equimolar pools of each library sample. DNAs were fragmented and ligated to Illumina adapters by “tagmentation.” After the amplification step, size selection was performed with AMPure XP Beads (Beckman Coulter, USA). The size distribution of fragments was checked using an Agilent DNA High Sensitivity chip (2100 Bionanalyzer, Agilent, USA). The libraries were sequenced on an Illumina HiSeq 2500 platform (Illumina, USA) run in paired-end reads in 2 × 100 bp using an Illumina Reagent Kit V2. The sequences were attributed to each index (8 bases) without considering any mismatches. Results demonstrated that the mean number of reads was 3.2 million and mean depth of coverage was 86×, as calculated on an estimated genome size of 4.5 Mb for M. tuberculosis. Quality assessment was performed with the use of the Prinseq-lite program (v.0.20.4) (http://prinseq.sourceforge.net) (8). Sequences from Illumina sequencing were joined using the FLASH program (v.1.2.11) (9). Illumina reads were loaded into Geneious Prime software (v.2021.2.2) (10) and trimmed with the BBDuk plugin (v.1.0, https://sourceforge.net/projects/bbmap/). Adapters on the right end and the low-quality ends (quality below 20%) were trimmed, while reads shorter than 200 bp were discarded. Then, the reads were subjected to preprocessing (https://www.geneious.com/tutorials/map-to-reference/). The genomes were assembled by using the “Map to reference” tool. As a reference genome, M. tuberculosis H37Rv (GenBank accession no. NC_000962.3) was used. A consensus sequence from aligned reads was extracted. We visually confirmed the circular genomes of the M. tuberculosis strains by assessing the reads spanning the junction between the two linearized ends and overlapping with them. Annotation was generated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (v.4.13) (11).
Data availability.
The Illumina raw sequencing reads and draft genomes of the 77 endemic multidrug-resistant M. tuberculosis strains of SIT41 (TUR) spoligotype from Bulgaria were deposited in GenBank under BioProject accession number PRJNA765918, SRA study number SRP339647, and BioSample accession numbers ranging between CP086331 to CP085542 and CP085617 (Table 1).
TABLE 1.
Descriptions and GenBank accession numbers of sequenced MDR Mycobacterium tuberculosis SIT41 (TUR) spoligotype strains from Bulgaria
| No. | M. tuberculosis strain/yr of isolation | Genome size (bp) | GC content (%) | No. of contigs (scaffolds) | N50 | No. of CDSa | No. of reads | Coverage (×) | Accession no. |
|
|---|---|---|---|---|---|---|---|---|---|---|
| GenBank | SRA | |||||||||
| 1 | 6/2009 | 4,418,129 | 65.9 | 133 (1) | 83,741 | 3,997 | 1,643,190 | 37.6 | CP085613 | SRR16149118 |
| 2 | 8/2009 | 4,417,820 | 65.5 | 110 (1) | 70,552 | 4,028 | 1,260,834 | 28.80 | CP085611 | SRR16149122 |
| 3 | 11/2009 | 4,417,016 | 65.5 | 107 (1) | 64,046 | 3,995 | 1,224,130 | 28.0 | CP085608 | SRR16149124 |
| 4 | 18/2009 | 4,418,290 | 65.0 | 130 (1) | 96,487 | 4,021 | 1,241,934 | 28.40 | CP085604 | SRR16149129 |
| 5 | 19/2009 | 4,418,358 | 65.5 | 118 (1) | 74,542 | 4,057 | 1,435,026 | 32.8 | CP085602 | SRR16149131 |
| 6 | 20/2009 | 4,423,816 | 65.8 | 110 (1) | 89,973 | 4,050 | 2,706,862 | 61.8 | CP085600 | SRR16149133 |
| 7 | 22/2009 | 4,419,048 | 65.3 | 115 (1) | 78,954 | 4,041 | 1,579,668 | 36.1 | CP085597 | SRR16149137 |
| 8 | 34/2009 | 4,418,147 | 65.5 | 101 (1) | 78,892 | 4,049 | 1,548,468 | 35.4 | CP085593 | SRR16149140 |
| 9 | 37/2009 | 4,417,302 | 65.4 | 102 (1) | 81,977 | 3,944 | 1,549,428 | 35.4 | CP085592 | SRR16149141 |
| 10 | 1/2010 | 4,421,044 | 65.1 | 119 (1) | 66,651 | 3,997 | 1,785,090 | 40.1 | CP085614 | SRR16149117 |
| 11 | 7/2010 | 4,417,102 | 65.0 | 120 (1) | 64,647 | 4,043 | 1,662,824 | 30.0 | CP085612 | SRR16149119 |
| 12 | 8/2010 | 4,416,514 | 65.0 | 143 (1) | 78,919 | 4,036 | 1,585,744 | 36.2 | CP085610 | SRR16149120 |
| 13 | 10/2010 | 4,426,983 | 65.1 | 122 (1) | 83,883 | 4,069 | 3,698,326 | 84.4 | CP085609 | SRR16149123 |
| 14 | 12/2010 | 4,416,642 | 65.1 | 115 (1) | 63,851 | 4,047 | 1,554,696 | 35.6 | CP085607 | SRR16149125 |
| 15 | 13/2010 | 4,421,011 | 65.6 | 104 (1) | 72,772 | 4,033 | 2,524,532 | 57.7 | CP085606 | SRR16149126 |
| 16 | 14/2010 | 4,417,911 | 64.9 | 127 (1) | 78,950 | 4,005 | 1,949,458 | 44.6 | CP085605 | SRR16149127 |
| 17 | 18/2010 | 4,432,448 | 65.4 | 105 (1) | 83,777 | 4,005 | 4,320,520 | 98.4 | CP085603 | SRR16149128 |
| 18 | 19/2010 | 4,418,613 | 64.9 | 119 (1) | 88,208 | 4,063 | 2,235,076 | 51.1 | CP085601 | SRR16149130 |
| 19 | 20/2010 | 4,417,343 | 65.3 | 122 (1) | 70,648 | 4,072 | 2,072,368 | 70.8 | CP085599 | SRR16149134 |
| 20 | 21/2010 | 4,417,666 | 65.0 | 103 (1) | 74,425 | 4,057 | 1,931,004 | 44.1 | CP085598 | SRR16149135 |
| 21 | 22/2010 | 4,420,383 | 65.0 | 103 (1) | 82,311 | 3,973 | 2,266,198 | 50.9 | CP085596 | SRR16149136 |
| 22 | 23/2010 | 4,420,918 | 65.1 | 107 (1) | 82,358 | 4,053 | 2,646,318 | 60.5 | CP085595 | SRR16149157 |
| 23 | 24/2010 | 4,420,288 | 65.0 | 117 (1) | 89,830 | 4,029 | 2,693,386 | 61.6 | CP085594 | SRR16149139 |
| 24 | 38/2010 | 4,419,478 | 65.1 | 118 (1) | 82,355 | 4,041 | 2,480,456 | 56.7 | CP085591 | SRR16149142 |
| 25 | 39/2010 | 4,419,821 | 65.0 | 113 (1) | 70,550 | 3,996 | 2,645,606 | 60.5 | CP085590 | SRR16149144 |
| 26 | 41/2010 | 4,419,996 | 65.2 | 124 (1) | 81,940 | 3,969 | 2,478,720 | 56.7 | CP085589 | SRR16149145 |
| 27 | 45/2010 | 4,423,281 | 64.9 | 126 (1) | 83,828 | 4,023 | 3,100,236 | 70.8 | CP085588 | SRR16149146 |
| 28 | 49/2010 | 4,419,930 | 65.1 | 108 (1) | 86,634 | 4,025 | 1,673,088 | 38.2 | CP085587 | SRR16149147 |
| 29 | 52/2010 | 4,420,722 | 64.7 | 112 (1) | 97,511 | 4,031 | 1,889,694 | 43.2 | CP085586 | SRR16149148 |
| 30 | 60/2010 | 4,419,012 | 65.0 | 112 (1) | 74,504 | 4,026 | 1,640,690 | 37.5 | CP085585 | SRR16149149 |
| 31 | 62/2010 | 4,420,147 | 64.9 | 120 (1) | 75,270 | 4,026 | 2,078,860 | 47.5 | CP085584 | SRR16149150 |
| 32 | 72/2010 | 4,418,098 | 65.0 | 100 (1) | 79,076 | 4,013 | 1,681,112 | 38.4 | CP085583 | SRR16149151 |
| 33 | 32/2011 | 4,425,788 | 64.9 | 254 (1) | 58,890 | 4,072 | 1,354,132 | 46.3 | CP085582 | SRR16149153 |
| 34 | 78/2011 | 4,417,082 | 65.4 | 254 (1) | 58,890 | 4,034 | 604,650 | 20.7 | CP086331 | SRR16149152 |
| 35 | 169/2011 | 4,435,970 | 64.7 | 116 (1) | 122,223 | 4,041 | 7,912,402 | 180.1 | CP085573 | SRR16149163 |
| 36 | 397/2013 | 4,439,340 | 64.7 | 128 (1) | 140,939 | 4,067 | 10,194,418 | 231.9 | CP085572 | SRR16149164 |
| 37 | 728/2015 | 4,440,561 | 64.9 | 170 (1) | 45,940 | 4,040 | 11,277,128 | 256.5 | CP085581 | SRR16149155 |
| 38 | 729/2015 | 4,431,948 | 65.1 | 137 (1) | 122,217 | 4,063 | 7,806,876 | 177.9 | CP085580 | SRR16149156 |
| 39 | 23/2016 | 4,433,118 | 65.1 | 122 (1) | 101,672 | 3,983 | 8,481,276 | 190.2 | CP085579 | SRR16149138 |
| 40 | 25/2016 | 4,434,896 | 65.0 | 124 (1) | 88,942 | 4,067 | 8,583,572 | 195.5 | CP085578 | SRR16149158 |
| 41 | 56/2016 | 4,427,560 | 65.0 | 139 (1) | 98,673 | 4,066 | 7,818,980 | 178.4 | CP085577 | SRR16149159 |
| 42 | 129/2016 | 4,430,911 | 65.1 | 134 (1) | 103,078 | 4,062 | 8,574,282 | 195.4 | CP085576 | SRR16149160 |
| 43 | 539/2016 | 4,440,780 | 64.8 | 119 (1) | 105,756 | 4,053 | 9,853,192 | 224.1 | CP085571 | SRR16149166 |
| 44 | 541/2016 | 4,429,660 | 65.0 | 109 (1) | 128,835 | 4,056 | 9,203,682 | 209.9 | CP085575 | SRR16149161 |
| 45 | 734/2016 | 4,427,845 | 64.9 | 132 (1) | 107,136 | 4,048 | 7,669,828 | 175.0 | CP085574 | SRR16149162 |
| 46 | 800/2016 | 4,440,527 | 64.5 | 123 (1) | 114,329 | 4,059 | 11,146,772 | 253.6 | CP085570 | SRR16149167 |
| 47 | 275/2017 | 4,419,700 | 64.9 | 163 (1) | 59,075 | 4,033 | 3,362,504 | 114.9 | CP085564 | SRR16149173 |
| 48 | 296/2017 | 4,418,199 | 65.0 | 155 (1) | 59,898 | 4,048 | 2,407,596 | 82.3 | CP085566 | SRR16149171 |
| 49 | 297/2017 | 4,418,725 | 64.9 | 149 (1) | 59,360 | 4,018 | 2,221,230 | 75.9 | CP085563 | SRR16149174 |
| 50 | 520/2017 | 4,418,006 | 65.0 | 165 (1) | 52,153 | 4,063 | 2,215,626 | 75.7 | CP085569 | SRR16149168 |
| 51 | 525/2017 | 4,418,536 | 64.9 | 165 (1) | 57,285 | 4,070 | 2,542,826 | 86.9 | CP085565 | SRR16149172 |
| 52 | 715/2017 | 4,420,895 | 65.1 | 255 (1) | 59,214 | 4,059 | 2,583,466 | 88.2 | CP085547 | SRR16149143 |
| 53 | 731/2017 | 4,419,645 | 65.2 | 157 (1) | 53,863 | 4,058 | 2,354,200 | 80.4 | CP085548 | SRR16149132 |
| 54 | 1207/2017 | 4,414,348 | 65.1 | 152 (1) | 47,575 | 4,067 | 1,472,358 | 50.4 | CP085542 | SRR16149188 |
| 55 | 1361/2017 | 4,416,102 | 65.0 | 172 (1) | 56,637 | 4,053 | 2,488,510 | 85.1 | CP085549 | SRR16149121 |
| 56 | 1400/2017 | 4,414,254 | 65.2 | 167 (1) | 53,201 | 4,050 | 1,770,318 | 60.6 | CP085550 | SRR16149113 |
| 57 | 1408/2017 | 4,414,653 | 65.1 | 166 (1) | 57,730 | 4,061 | 1,759,172 | 60.2 | CP085567 | SRR16149170 |
| 58 | 300/2017 | 4,415,628 | 65.0 | 152 (1) | 52,153 | 4,064 | 1,202,309 | 41.1 | CP085568 | SRR16149169 |
| 59 | 392/2018 | 4,418,914 | 64.9 | 152 (1) | 74,473 | 4,054 | 2,777,068 | 94.9 | CP085557 | SRR16149181 |
| 60 | 405/2018 | 4,418,415 | 64.9 | 145 (1) | 59,406 | 4,070 | 2,331,796 | 79.7 | CP085551 | SRR16149112 |
| 61 | 416/2018 | 4,418,171 | 64.9 | 172 (1) | 55,994 | 4,075 | 1,995,066 | 68.2 | CP085559 | SRR16149179 |
| 62 | 425/2018 | 4,418,046 | 64.9 | 146 (1) | 66,999 | 4,058 | 2,593,182 | 88.7 | CP085558 | SRR16149180 |
| 63 | 431/2018 | 4,420,078 | 64.9 | 144 (1) | 57,124 | 4,057 | 2,570,998 | 87.8 | CP085546 | SRR16149154 |
| 64 | 525/2018 | 4,417,688 | 65.0 | 170 (1) | 51,868 | 4,052 | 2,274,844 | 77.8 | CP085562 | SRR16149175 |
| 65 | 537/2018 | 4,417,657 | 64.8 | 161 (1) | 57,388 | 4,080 | 2,128,110 | 72.7 | CP085556 | SRR16149182 |
| 66 | 543/2018 | 4,419,294 | 64.8 | 150 (1) | 56,146 | 4,080 | 2,194,518 | 75.0 | CP085554 | SRR16149184 |
| 67 | 545/2018 | 4,419,615 | 64.8 | 151 (1) | 64,246 | 4,082 | 2,528,728 | 86.4 | CP085552 | SRR16149186 |
| 68 | 816/2018 | 4,417,436 | 65.0 | 146 (1) | 61,065 | 4,067 | 2,191,714 | 74.9 | CP085561 | SRR16149177 |
| 69 | 993/2018 | 4,415,299 | 65.0 | 152 (1) | 58,168 | 4,042 | 2,494,242 | 85.3 | CP085560 | SRR16149178 |
| 70 | 1072/2018 | 4,415,762 | 65.0 | 149 (1) | 56,052 | 4,065 | 2,358,978 | 80.7 | CP085555 | SRR16149183 |
| 71 | 1168/2018 | 4,414,894 | 65.0 | 147 (1) | 62,519 | 4,039 | 1,863,456 | 63.7 | CP085553 | SRR16149185 |
| 72 | 253/2019 | 4,476,622 | 65.2 | 112 (1) | 98,635 | 4,056 | 3,753,884 | 125.8 | CP085615 | SRR16149116 |
| 73 | 270/2019 | 4,420,676 | 65.1 | 150 (1) | 56,699 | 4,050 | 2,865,294 | 97.9 | CP085545 | SRR16149165 |
| 74 | 293/2019 | 4,447,276 | 66.0 | 111 (1) | 88,142 | 4,060 | 3,180,676 | 107.3 | CP085616 | SRR16149115 |
| 75 | 546/2019 | 4,444,377 | 66.0 | 96 (1) | 83,190 | 4,048 | 2,837,276 | 95.8 | CP085617 | SRR16149114 |
| 76 | 598/2019 | 4,420,900 | 65.1 | 147 (1) | 73,760 | 4,061 | 2,948,322 | 100.7 | CP085544 | SRR16149176 |
| 77 | 952/2019 | 4,420,797 | 65.0 | 148 (1) | 64,230 | 4,021 | 3,012,618 | 102.9 | CP085543 | SRR16149187 |
CDS, coding DNA sequences.
ACKNOWLEDGMENTS
This work was supported by the Bulgarian National Science Fund (BNSF) with grant N: DN13/4-15.12.2017 and by the European Fund for Regional Development through the Operational Program Science and Education for Smart Growth 2014 to 2020, grant no. BG05M2OP001-1.002-0001-C04. We thank Elizabeta Bachiyska, Yuliana Atanasova, Anna Baykova, and Stanislava Yordanova from NRL for Tuberculosis at NCIPD, Sofia, Bulgaria for providing isolates and drug susceptibility testing of M. tuberculosis strains.
Contributor Information
Stefan Panaiotov, Email: spanaiotov@yahoo.com.
Julie C. Dunning Hotopp, University of Maryland School of Medicine
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The Illumina raw sequencing reads and draft genomes of the 77 endemic multidrug-resistant M. tuberculosis strains of SIT41 (TUR) spoligotype from Bulgaria were deposited in GenBank under BioProject accession number PRJNA765918, SRA study number SRP339647, and BioSample accession numbers ranging between CP086331 to CP085542 and CP085617 (Table 1).
TABLE 1.
Descriptions and GenBank accession numbers of sequenced MDR Mycobacterium tuberculosis SIT41 (TUR) spoligotype strains from Bulgaria
| No. | M. tuberculosis strain/yr of isolation | Genome size (bp) | GC content (%) | No. of contigs (scaffolds) | N50 | No. of CDSa | No. of reads | Coverage (×) | Accession no. |
|
|---|---|---|---|---|---|---|---|---|---|---|
| GenBank | SRA | |||||||||
| 1 | 6/2009 | 4,418,129 | 65.9 | 133 (1) | 83,741 | 3,997 | 1,643,190 | 37.6 | CP085613 | SRR16149118 |
| 2 | 8/2009 | 4,417,820 | 65.5 | 110 (1) | 70,552 | 4,028 | 1,260,834 | 28.80 | CP085611 | SRR16149122 |
| 3 | 11/2009 | 4,417,016 | 65.5 | 107 (1) | 64,046 | 3,995 | 1,224,130 | 28.0 | CP085608 | SRR16149124 |
| 4 | 18/2009 | 4,418,290 | 65.0 | 130 (1) | 96,487 | 4,021 | 1,241,934 | 28.40 | CP085604 | SRR16149129 |
| 5 | 19/2009 | 4,418,358 | 65.5 | 118 (1) | 74,542 | 4,057 | 1,435,026 | 32.8 | CP085602 | SRR16149131 |
| 6 | 20/2009 | 4,423,816 | 65.8 | 110 (1) | 89,973 | 4,050 | 2,706,862 | 61.8 | CP085600 | SRR16149133 |
| 7 | 22/2009 | 4,419,048 | 65.3 | 115 (1) | 78,954 | 4,041 | 1,579,668 | 36.1 | CP085597 | SRR16149137 |
| 8 | 34/2009 | 4,418,147 | 65.5 | 101 (1) | 78,892 | 4,049 | 1,548,468 | 35.4 | CP085593 | SRR16149140 |
| 9 | 37/2009 | 4,417,302 | 65.4 | 102 (1) | 81,977 | 3,944 | 1,549,428 | 35.4 | CP085592 | SRR16149141 |
| 10 | 1/2010 | 4,421,044 | 65.1 | 119 (1) | 66,651 | 3,997 | 1,785,090 | 40.1 | CP085614 | SRR16149117 |
| 11 | 7/2010 | 4,417,102 | 65.0 | 120 (1) | 64,647 | 4,043 | 1,662,824 | 30.0 | CP085612 | SRR16149119 |
| 12 | 8/2010 | 4,416,514 | 65.0 | 143 (1) | 78,919 | 4,036 | 1,585,744 | 36.2 | CP085610 | SRR16149120 |
| 13 | 10/2010 | 4,426,983 | 65.1 | 122 (1) | 83,883 | 4,069 | 3,698,326 | 84.4 | CP085609 | SRR16149123 |
| 14 | 12/2010 | 4,416,642 | 65.1 | 115 (1) | 63,851 | 4,047 | 1,554,696 | 35.6 | CP085607 | SRR16149125 |
| 15 | 13/2010 | 4,421,011 | 65.6 | 104 (1) | 72,772 | 4,033 | 2,524,532 | 57.7 | CP085606 | SRR16149126 |
| 16 | 14/2010 | 4,417,911 | 64.9 | 127 (1) | 78,950 | 4,005 | 1,949,458 | 44.6 | CP085605 | SRR16149127 |
| 17 | 18/2010 | 4,432,448 | 65.4 | 105 (1) | 83,777 | 4,005 | 4,320,520 | 98.4 | CP085603 | SRR16149128 |
| 18 | 19/2010 | 4,418,613 | 64.9 | 119 (1) | 88,208 | 4,063 | 2,235,076 | 51.1 | CP085601 | SRR16149130 |
| 19 | 20/2010 | 4,417,343 | 65.3 | 122 (1) | 70,648 | 4,072 | 2,072,368 | 70.8 | CP085599 | SRR16149134 |
| 20 | 21/2010 | 4,417,666 | 65.0 | 103 (1) | 74,425 | 4,057 | 1,931,004 | 44.1 | CP085598 | SRR16149135 |
| 21 | 22/2010 | 4,420,383 | 65.0 | 103 (1) | 82,311 | 3,973 | 2,266,198 | 50.9 | CP085596 | SRR16149136 |
| 22 | 23/2010 | 4,420,918 | 65.1 | 107 (1) | 82,358 | 4,053 | 2,646,318 | 60.5 | CP085595 | SRR16149157 |
| 23 | 24/2010 | 4,420,288 | 65.0 | 117 (1) | 89,830 | 4,029 | 2,693,386 | 61.6 | CP085594 | SRR16149139 |
| 24 | 38/2010 | 4,419,478 | 65.1 | 118 (1) | 82,355 | 4,041 | 2,480,456 | 56.7 | CP085591 | SRR16149142 |
| 25 | 39/2010 | 4,419,821 | 65.0 | 113 (1) | 70,550 | 3,996 | 2,645,606 | 60.5 | CP085590 | SRR16149144 |
| 26 | 41/2010 | 4,419,996 | 65.2 | 124 (1) | 81,940 | 3,969 | 2,478,720 | 56.7 | CP085589 | SRR16149145 |
| 27 | 45/2010 | 4,423,281 | 64.9 | 126 (1) | 83,828 | 4,023 | 3,100,236 | 70.8 | CP085588 | SRR16149146 |
| 28 | 49/2010 | 4,419,930 | 65.1 | 108 (1) | 86,634 | 4,025 | 1,673,088 | 38.2 | CP085587 | SRR16149147 |
| 29 | 52/2010 | 4,420,722 | 64.7 | 112 (1) | 97,511 | 4,031 | 1,889,694 | 43.2 | CP085586 | SRR16149148 |
| 30 | 60/2010 | 4,419,012 | 65.0 | 112 (1) | 74,504 | 4,026 | 1,640,690 | 37.5 | CP085585 | SRR16149149 |
| 31 | 62/2010 | 4,420,147 | 64.9 | 120 (1) | 75,270 | 4,026 | 2,078,860 | 47.5 | CP085584 | SRR16149150 |
| 32 | 72/2010 | 4,418,098 | 65.0 | 100 (1) | 79,076 | 4,013 | 1,681,112 | 38.4 | CP085583 | SRR16149151 |
| 33 | 32/2011 | 4,425,788 | 64.9 | 254 (1) | 58,890 | 4,072 | 1,354,132 | 46.3 | CP085582 | SRR16149153 |
| 34 | 78/2011 | 4,417,082 | 65.4 | 254 (1) | 58,890 | 4,034 | 604,650 | 20.7 | CP086331 | SRR16149152 |
| 35 | 169/2011 | 4,435,970 | 64.7 | 116 (1) | 122,223 | 4,041 | 7,912,402 | 180.1 | CP085573 | SRR16149163 |
| 36 | 397/2013 | 4,439,340 | 64.7 | 128 (1) | 140,939 | 4,067 | 10,194,418 | 231.9 | CP085572 | SRR16149164 |
| 37 | 728/2015 | 4,440,561 | 64.9 | 170 (1) | 45,940 | 4,040 | 11,277,128 | 256.5 | CP085581 | SRR16149155 |
| 38 | 729/2015 | 4,431,948 | 65.1 | 137 (1) | 122,217 | 4,063 | 7,806,876 | 177.9 | CP085580 | SRR16149156 |
| 39 | 23/2016 | 4,433,118 | 65.1 | 122 (1) | 101,672 | 3,983 | 8,481,276 | 190.2 | CP085579 | SRR16149138 |
| 40 | 25/2016 | 4,434,896 | 65.0 | 124 (1) | 88,942 | 4,067 | 8,583,572 | 195.5 | CP085578 | SRR16149158 |
| 41 | 56/2016 | 4,427,560 | 65.0 | 139 (1) | 98,673 | 4,066 | 7,818,980 | 178.4 | CP085577 | SRR16149159 |
| 42 | 129/2016 | 4,430,911 | 65.1 | 134 (1) | 103,078 | 4,062 | 8,574,282 | 195.4 | CP085576 | SRR16149160 |
| 43 | 539/2016 | 4,440,780 | 64.8 | 119 (1) | 105,756 | 4,053 | 9,853,192 | 224.1 | CP085571 | SRR16149166 |
| 44 | 541/2016 | 4,429,660 | 65.0 | 109 (1) | 128,835 | 4,056 | 9,203,682 | 209.9 | CP085575 | SRR16149161 |
| 45 | 734/2016 | 4,427,845 | 64.9 | 132 (1) | 107,136 | 4,048 | 7,669,828 | 175.0 | CP085574 | SRR16149162 |
| 46 | 800/2016 | 4,440,527 | 64.5 | 123 (1) | 114,329 | 4,059 | 11,146,772 | 253.6 | CP085570 | SRR16149167 |
| 47 | 275/2017 | 4,419,700 | 64.9 | 163 (1) | 59,075 | 4,033 | 3,362,504 | 114.9 | CP085564 | SRR16149173 |
| 48 | 296/2017 | 4,418,199 | 65.0 | 155 (1) | 59,898 | 4,048 | 2,407,596 | 82.3 | CP085566 | SRR16149171 |
| 49 | 297/2017 | 4,418,725 | 64.9 | 149 (1) | 59,360 | 4,018 | 2,221,230 | 75.9 | CP085563 | SRR16149174 |
| 50 | 520/2017 | 4,418,006 | 65.0 | 165 (1) | 52,153 | 4,063 | 2,215,626 | 75.7 | CP085569 | SRR16149168 |
| 51 | 525/2017 | 4,418,536 | 64.9 | 165 (1) | 57,285 | 4,070 | 2,542,826 | 86.9 | CP085565 | SRR16149172 |
| 52 | 715/2017 | 4,420,895 | 65.1 | 255 (1) | 59,214 | 4,059 | 2,583,466 | 88.2 | CP085547 | SRR16149143 |
| 53 | 731/2017 | 4,419,645 | 65.2 | 157 (1) | 53,863 | 4,058 | 2,354,200 | 80.4 | CP085548 | SRR16149132 |
| 54 | 1207/2017 | 4,414,348 | 65.1 | 152 (1) | 47,575 | 4,067 | 1,472,358 | 50.4 | CP085542 | SRR16149188 |
| 55 | 1361/2017 | 4,416,102 | 65.0 | 172 (1) | 56,637 | 4,053 | 2,488,510 | 85.1 | CP085549 | SRR16149121 |
| 56 | 1400/2017 | 4,414,254 | 65.2 | 167 (1) | 53,201 | 4,050 | 1,770,318 | 60.6 | CP085550 | SRR16149113 |
| 57 | 1408/2017 | 4,414,653 | 65.1 | 166 (1) | 57,730 | 4,061 | 1,759,172 | 60.2 | CP085567 | SRR16149170 |
| 58 | 300/2017 | 4,415,628 | 65.0 | 152 (1) | 52,153 | 4,064 | 1,202,309 | 41.1 | CP085568 | SRR16149169 |
| 59 | 392/2018 | 4,418,914 | 64.9 | 152 (1) | 74,473 | 4,054 | 2,777,068 | 94.9 | CP085557 | SRR16149181 |
| 60 | 405/2018 | 4,418,415 | 64.9 | 145 (1) | 59,406 | 4,070 | 2,331,796 | 79.7 | CP085551 | SRR16149112 |
| 61 | 416/2018 | 4,418,171 | 64.9 | 172 (1) | 55,994 | 4,075 | 1,995,066 | 68.2 | CP085559 | SRR16149179 |
| 62 | 425/2018 | 4,418,046 | 64.9 | 146 (1) | 66,999 | 4,058 | 2,593,182 | 88.7 | CP085558 | SRR16149180 |
| 63 | 431/2018 | 4,420,078 | 64.9 | 144 (1) | 57,124 | 4,057 | 2,570,998 | 87.8 | CP085546 | SRR16149154 |
| 64 | 525/2018 | 4,417,688 | 65.0 | 170 (1) | 51,868 | 4,052 | 2,274,844 | 77.8 | CP085562 | SRR16149175 |
| 65 | 537/2018 | 4,417,657 | 64.8 | 161 (1) | 57,388 | 4,080 | 2,128,110 | 72.7 | CP085556 | SRR16149182 |
| 66 | 543/2018 | 4,419,294 | 64.8 | 150 (1) | 56,146 | 4,080 | 2,194,518 | 75.0 | CP085554 | SRR16149184 |
| 67 | 545/2018 | 4,419,615 | 64.8 | 151 (1) | 64,246 | 4,082 | 2,528,728 | 86.4 | CP085552 | SRR16149186 |
| 68 | 816/2018 | 4,417,436 | 65.0 | 146 (1) | 61,065 | 4,067 | 2,191,714 | 74.9 | CP085561 | SRR16149177 |
| 69 | 993/2018 | 4,415,299 | 65.0 | 152 (1) | 58,168 | 4,042 | 2,494,242 | 85.3 | CP085560 | SRR16149178 |
| 70 | 1072/2018 | 4,415,762 | 65.0 | 149 (1) | 56,052 | 4,065 | 2,358,978 | 80.7 | CP085555 | SRR16149183 |
| 71 | 1168/2018 | 4,414,894 | 65.0 | 147 (1) | 62,519 | 4,039 | 1,863,456 | 63.7 | CP085553 | SRR16149185 |
| 72 | 253/2019 | 4,476,622 | 65.2 | 112 (1) | 98,635 | 4,056 | 3,753,884 | 125.8 | CP085615 | SRR16149116 |
| 73 | 270/2019 | 4,420,676 | 65.1 | 150 (1) | 56,699 | 4,050 | 2,865,294 | 97.9 | CP085545 | SRR16149165 |
| 74 | 293/2019 | 4,447,276 | 66.0 | 111 (1) | 88,142 | 4,060 | 3,180,676 | 107.3 | CP085616 | SRR16149115 |
| 75 | 546/2019 | 4,444,377 | 66.0 | 96 (1) | 83,190 | 4,048 | 2,837,276 | 95.8 | CP085617 | SRR16149114 |
| 76 | 598/2019 | 4,420,900 | 65.1 | 147 (1) | 73,760 | 4,061 | 2,948,322 | 100.7 | CP085544 | SRR16149176 |
| 77 | 952/2019 | 4,420,797 | 65.0 | 148 (1) | 64,230 | 4,021 | 3,012,618 | 102.9 | CP085543 | SRR16149187 |
CDS, coding DNA sequences.