3.2. Genome size, organization, and ORFs
The libraries were prepared from the isolated DNA sample by Truseq Nano DNA Library preparation kit. The number of filtered reads obtained was 24,657,026 out of which 1,241,516 reads were mapped to LSDV-NI2490 strain with 99.9% coverage using the CLC genomics workbench. The average size of libraries was 442 bp, whereas the average coverage depth was ~2500 X. After reference mapping and denovo assembly and calling the consensus from the resultant BAM file, the full-length genome size of LSDV-WB/IND/19 was 150,969 bp with a 145,938 bp central coding region flanked by two inverted terminal repeats (ITRs) of 2613 bp and 2418 bp. The genome has a high A+T content of 74.1% and a compact gene arrangement with no large regions of non-coding sequence as noted previously (Tulman et al., 2001; Biswas et al., 2020). The putative concatemer resolution sequence (CRS) element (5′‐ ATTTATAGGCTAAAAAAAAAGTA‐3′) was present at nt positions 86-108 which is a highly conserved sequence necessary for concatemer resolution during genome replication. A total of 156 ORFs were annotated as putative genes and numbered from left to right as previously described (Tulman et al., 2001; Biswas et al., 2020). Four genes each, viz. LSD_001 and LSD_156, LSD_002 and LSD_155, LSD_003 and LSD_154, and LSD_004 and LSD_153 are identical and appear twice due to their location within the ITRs. Like other LSDVs, LSDV-WB/IND/19 encodes nine genes (LSD_002, LSD_004, LSD_009, LSD_013, LSD_026, LSD_126, LSD_132, LSD_153, LSD_155) that have been disrupted by accumulated mutations in GTPV and SPPV. Although, the total sequence length remains largely unchanged among capripoxviruses. Two short open reading frames located between genes 28/29 and120/121, encoding 49‐a.a. and 41‐a.a. proteins, respectively were numbered LSD_028.5 and LSD_120.5 as described previously (Biswas et al., 2020).