Full length genome sequence of Polish isolate of Beet soil-borne virus confirms low level of genetic diversity.

Abstract

The complete nucleotide sequence of a Polish isolate of Beet soil-borne virus was determined for the first time. The genome organization was identical with those previously established for isolates from Germany and China. A comparison of the Polish isolate with others deposited in GenBank revealed high level of nucleotide identity, about 98-100%, throughout the genome analyzed. The ratio between non-synonymous and synonymous substitutions was rather low suggesting a negative selective pressure. The non-synonymous mutations were particulary frequent in triple gene block.

Complete Genomic Characterization of Two Beet Soil-Borne Virus Isolates from Turkey: Implications of Comparative Analysis of Genome Sequences

“…This finding is in line with that of other studies ( Borodynko et al, 2009 ; Koenig et al, 2000 ; Wang et al, 2008 ). Consistent with previous studies ( Borodynko et al, 2009 ; Wang et al, 2008 ), our results revealed that TGB3 (Pi = 0.034) was a more variable gene region than TGB1 and TGB2. Sequence diversity in the 5′-UTRs and 3′-UTRs of RNA1 and RNA3 were relatively higher than those of RNA2 ( Supplementary Table 1 ).…”

“…MN087414, MN087415, and MN087416 for RNAs 1, 2, and 3, respectively) were determined. The genome organization and base composition of both isolates were similar to other BSBV isolates ( Borodynko et al, 2009 ; Camelo-Garcia et al, 2019 ; Crutzen et al, 2009 ; Koenig and Loss, 1997 ; Koenig et al, 1996 , 1997 ; Wang et al, 2008 ).…”

“…MN087414, MN087415, and MN087416 for RNAs 1, 2, and 3, respectively) were determined. The genome organization and base composition of both isolates were similar to other BSBV isolates (Borodynko et al, 2009;Camelo-Garcia et al, 2019;Crutzen et al, 2009;Koenig et al, 1996Wang et al, 2008). RNA1 of BSBV-TR1 and -TR3 consisted of 5,835 nt and contained the putative viral replicase domain with conserved motifs methyltransferase (MetT), helicase (Hel) and RNA-dependent RNA polymerase (RdRP).…”

“…Understanding the distribution of genetic diversity among individuals, populations, and gene pools are crucial for the efficient management of germplasm collections and breeding programs ( Borodynko et al, 2009 ). According to prior studies, BSBV isolates are highly conserved regarding sequence variation and evolutionary divergence ( Borodynko et al, 2009 ; Wang et al, 2008 ). Our sequence analysis confirmed that all BSBV isolates identified to date are closely related to each other and relatively conserved, particularly in the case of RNA1 (Pi = 0.02513).…”

“…According to sequence identity analyses, Turkish isolates were most closely related to the BSBV isolates reported from Iran (97.83% to 98.77% nt identity). The overall variability observed in BSBV worldwide suggested high genetic stability that could be explained by the ecological bottleneck imposed by vectors and host plants which reduce the genetic variation of the virus population ( Borodynko et al, 2009 ). The replicase and CPRT cistrons accumulated the largest number of mutations whereas the TGB2 region harbored the lowest number of mutations.…”