High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL

Abstract

The genus Synedrella remains monotypic in spite of its wide range of distribution, in which S. nodiflora (L.) Gaertn has taxonomically been the only member of the genus so far. This leads to assumption of the very low genetic difference among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB-rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpBrbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) as well as low haplotype diversity (0.0345) and low nucleotide diversity (0.000040). In addition, the very low fixation index (FST = 0.02645; p = 1.00000) proves low genetic difference, or in other words, indicates high connectivity among populations of S. nodiflora in Java Island. At the same time provides a fact of nearly no variation among the IGS atpB -rbcL sequences. (Chiang & Schaal, 2000a, 2000bFujii et al., 1997;Small et al., 2005;Taberlet et al., 1991). How to CiteThe purpose of this study is to know genetic diversity and the level of connectivity among S. nodiflora populations in Java Island based on IGS atpB -rbcL. It is expected from the study that molecular data can be obtained to compare with the existing taxonomical status of the species as the only member of genus Synedrella, which has been based merely on phenotypical characters. METHODSS. nodiflora samples were collected randomly from ten different locations in Java Island, i.e. Bogor (n = 5), Tasikmalaya (n = 5), Ciamis (n = 5), Banyumas (n = 10), Yogyakarta (n = 5), Mojokerto (n = 5), Probolinggo (n = 6), Malang (n = 6), Lumajang (n = 5) and Jember (n = 6) ( Figure 1). The plants were taken with their roots and were put into plastic bottles previously filled with a little water prior to be planted in pots in a glass house. Genomic DNAs were isolated from uppermost leaves following CTAB method (Doyle & Doyle, 1990). The quality and quantity of the isolated DNAs were measured using genequant. Amplification of IGS atpB -rbcL was performed using universal primers, i.e. 5'-ACA TCK ART ACK GGA CCA ATA A-3' as forward primer and 5' -AAC ACC AGC TTT RAA TCC AA-3' as reverse primer (Chiang et al., 1998). A total volume of 11.5 µl PCR mixture consisting of 2 µl template DNA, 5 µl KapaTaq DNA polymerase, 4.25 µl nuclease free water (NFW) and 0.125 µl of individual primer was subjected to PCR condition as follows: pre-denaturation of 94

Weeds Associated with Papaya Plants (Carica Papaya L.) in Bengkulu

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Genetic variability and phylogenetic relationships of Begonia multangula based on atpB-rbcL non-coding spacer of cpDNA sequences

“…This research reveals that atpB-rbcL IGS sequence variation in the Java, Bali, and Sumatera population of B. multangula, similar to atpB-rbcL IGS sequence variation of Synedrella nodiflora (L.) Gaertn. populations in Java Island (Susanto et al 2018), Pistachia vera L. (Talebi et al 2016). However, in several plant species populations, atpB-rbcL intergenic spacer sequences were very variable.…”

“…The cpDNA regions are extensively utilized as markers in phylogenetic and phylogeographic research. The atpB-rbcL spacer, which is located between the large subunit of the ribulose-1-5bisphosphate-carboxylase (rbcL) and the beta subunit of the chloroplast ATP-synthase (atpB) genes, has been beneficial in evolutionary studies of angiosperms (Susanto et al 2018).…”

Molecular characteristics of two phenotypically identical species of Asteraceae based on the intergenic spacer trnT(UGU)-trnL(UAA)

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