Pepper yellow leaf curl Indonesia virus (PepYLCIV), a bipartite begomovirus transmitted by Bemisia tabaci, is a major viral pathogen affecting chili pepper production in Indonesia. Although complete genome sequences are available for several pepper yellow leaf curl viruses, comparative evolutionary analyses across all recognized species remain limited. This study generated complete genome sequences for 3 PepYLCIV isolates using Oxford Nanopore sequencing and analyzed them together with publicly available genomes representing 4 recognized pepper yellow leaf curl virus species. The 3 isolates displayed the typical bipartite genome organization of PepYLCIV. Comparative genome analyses detected 14 recombination events in DNA-A and 9 in DNA-B, indicating that recombination has contributed substantially to genome diversification. Phylogenetic reconstruction and pairwise nucleotide identity analyses consistently placed the newly sequenced isolates within the PepYLCIV clade and resolved the 4 virus species as distinct evolutionary groups. Among the species examined, PepYLCIV showed the highest level of nucleotide diversity. Selection analyses indicated stronger purifying selection acting on DNA-A (ω = 0.049–0.111) than on DNA-B (ω = 0.768–0.839), consistent with the greater sequence variability of DNA-B. Population genetic analyses also revealed marked genetic differentiation among species (βFST = 0.765–0.991 for DNA-A and 0.751 for DNA-B). These findings expand the genomic resources available for PepYLCIV, provide new insights into the evolution of pepper yellow leaf curl viruses, and support future epidemiological surveillance, molecular detection, and resistance breeding in chili pepper.
Y. B. Paradisa, K. Mutaqin, M. Syukur et al.· Caraka Tani: Journal of Sust...· 0 citations
Abstract. Sahid ZD, Qadir A, Syukur M, Ariyanto KF, Wijaya AK, Suwarno PM, Rusmiyati H, Hatta ANNL. 2026. Quantitative and qualitative morphological diversity among nine cherry tomato (Solanum lycopersicum) genotypes grown under lowland conditions. Biodiversitas 27 (6): d270622. https://doi.org/10.13057/biodiv/d270622. Cherry tomatoes are a type of tomato that has seen increasing market demand post-global pandemic as a healthy fruit. Cherry tomato cultivation is generally carried out in highlands and faces competition from other vegetable cultivation. Therefore, developing cherry tomato varieties adapted to lowland conditions is necessary. Developing new superior varieties requires basic information for selecting the diversity of the parents used. Therefore, this study aims to evaluate the morphological diversity of Institut Pertanian Bogor (IPB) cherry tomato lines as cross-breeding parents in further studies. The study was conducted at the lowland greenhouse teaching factory of the vocational school, Institut Pertanian Bogor, Bogor, using automated irrigation and fertigation systems and a single-factor randomized complete block design. The results of this study indicate that there is diversity among nine Institut Pertanian Bogor cherry tomato lines (hybrid and non-hybrid lines) that have the potential to be used as parents in the development of new superior varieties. The seed germination percentage measured in this study varied (80-95%), with early flowering and harvest times (26 and 62 days after transplanting). The average fruit length, diameter, and weight (3.28 cm, 19.24 mm, and 7.23 g) measured in this study showed a vast morphological divergence, making them potential parent lines in cherry tomato breeding. Cluster analysis of nine genotypes based on their morphological characteristics resulted in three main groups, from which parents for breeding were selected. IPBTC 147 forms a distinct group due to its unique morphological characteristics, both quantitative and qualitative, which significantly differ from other genotypes, particularly in its fruit shape and color. This genotype has an average fruit weight of 5 g with the longest fruit stalk length (2.27 cm). The yellow color of this fruit has the potential to produce high diversity in the F2 when crossed with red fruit color. The morphological performance information of this research is expected to serve as a consideration for selecting parents for the development of cherry tomatoes adapted to lowlands.
Z. D. Sahid, Abdul Qadir, M. Syukur et al.· Biodiversitas Journal of Bio...· 0 citations
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