Fig. 1
Change of the BLV integration sites during the course of disease progression in a BLV naturally-infected cow. A Summary of the integration sites detected in Stage I, Stage II, and Stage III, respectively. 1Chr, Chromosome. 2D.P, Duplicated Nucleotide. 3L, left read; R, right read; red color, duplicated nucleotide sequence; upper case, nucleotide sequence of the cattle; lower case, nucleotide sequence of the BLV; bold letter, different sequence compared to the reference sequence; –, deleted sequence compared to the reference sequence. 4CAPN7, calpain 7; ACER2, alkaline ceramidase 2; DCAF12, DDB1 and CUL4 associated factor 12; TMEM231, transmembrane protein 231; NPR3, natriuretic peptide receptor 3; FHIT, fragile histidine triad diadenosine triphosphatase; ASPHD1, aspartate beta-hydroxylase domain containing 1; SGMS1, sphingomyelin synthase 1; DNMBP, dynamin binding protein; POGK, pogo transposable element derived with KRAB domain; FAM78B, family with sequence similarity 78 member B; SF3B5, splicing factor 3b subunit 5; UTRN, utrophin; NDUFAF6, NADH:ubiquinone oxidoreductase complex assembly factor 6; TP53INP1, tumor protein p53 inducible nuclear protein 1; PGR, progesterone receptor; CCDC82, coiled-coil domain containing 82; COA6, cytochrome c oxidase assembly factor 6; TOMM20, translocase of outer mitochondrial membrane 20; NBEAL1, neurobeachin like 1; CHEK2, checkpoint kinase 2; CLRN1, clarin 1; SIAH2, siah E3 ubiquitin protein ligase 2; REEP6, receptor accessory protein 6; MBD3, methyl-CpG binding domain protein 3; ABCA1, ATP binding cassette subfamily A member 1; FSD1L, fibronectin type III and SPRY domain containing 1 like; TREM1, triggering receptor expressed on myeloid cells 1; FOXP4, forkhead box P4. 5Low Complexity, Low complexity repeats; SINE, Short interspersed nuclear elements; DNA, DNA repeat elements; LTR, Long terminal repeat elements. B Pie charts showing the relative abundance of each sample at various disease progression from a BLV-infected cow in Stages I, II, and III, respectively. The numbers of integration site represent each of the detected clone in Fig. 1 were described. State of clonal expansion of cells carrying the integration site and massive depletion of cells carrying the integration site, and clinical stage of disease progression of Stages I, II, and III from one BLV-infected cow, respectively, indicated