Phylogenetic Relationships of Sugarcane Related Genera and Species Based on ITS Sequences of Nuclear Ribosomal DNA

Liu, Xin-long; Su, Huo-Sheng; Ma, Lan; Lü, Xin; XiongMei, Ying; Cai, Qingsheng; YuanHong, Fan

doi:10.3724/sp.j.1006.2010.01853

Cited by 4 publications

(5 citation statements)

References 10 publications

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“…The result is obtained in the present study have shown that GC percentage is lower in ITS1 compare to ITS2 and also sequence length is longer in ITS-2 region than in ITS-1. A similar result was reported by [18,42], but in the present investigation, the variation sites found higher in ITS-2 region than ITS-1 as is observed in other plants [16,43]. The possible reason behind that the spp.…”

Section: Discussionsupporting

confidence: 91%

Assessment of genetic diversity among different sugarcane genotypes using internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA)

Forough

Shivaji

Mallikarjun

2018

GSC Biol. and Pharm. Sci.

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Internal transcribed spacer or ITS region of nuclear ribosomal DNA (rDNA) has been used to evaluate genetic assortment and phylogenetic relationship in nine sugarcane genotypes including Saccharum species and another related genus as Erianthus, Narenga and hybrid. DNA was extracted from selected genotypes and ITS (ITS-1 and ITS-2) regions were amplified using specific primers. The sequence lengths ITS-1 showed 205-207 bp, while ITS2 was ranged from 211-218 bp. However, G+C content (%) 65.2% -67% in ITS-1 and in ITS-2 68.4% -99.7%. The sequence lengths of fragment and GC content of ITS-1 and ITS-2 regions showed variable. To evaluate the phylogenetic association of both the region of ITS (ITS-1 and ITS-2) neighbor-joining (NJ) method was employed. The cluster A of ITS-1 and cluster B for ITS-2 and cluster C combined between ITS1+ ITS2 sequences gave two distinct groups A and B. The group A represented the ITS1 sequences which showed two subgroups I and II. The A-I subgroup consisted of wild species of sugarcane; Erianthus, Narenga and S. robustum, whereas the A-II subgroup consisted of the Saccharum species and hybrid. The ITS2 sequences in the group B showed better correlation amongst each other. The sequences ITS-1 & ITS-2 combined and compared with some selected sequences from NCBI database using NJ method. The results have confirmed that ITS region can be used for evaluating the genetic assortment in Saccharum and its closely related genes.

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Section: Discussionsupporting

confidence: 91%

Assessment of genetic diversity among different sugarcane genotypes using internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA)

Forough

Shivaji

Mallikarjun

2018

GSC Biol. and Pharm. Sci.

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“…In addition, our clusering analysis revealed that the accessions of the two species in each branch were mixed and without distinct boundaries. These findings were consistent with the phylogenetic trees of Miscanthus and related genera inferred from ITS sequences (Hodkinson et al 2002b, Chen et al 2007, Liu et al 2010), SSR markers (Ge et al 2017), SNPs (Clark et al 2014) and the dataset of genome size, ploidy level and genomic polymorphisms (Chae et al 2014). To summarise, our clustering results have demonstrated that there was a very close phylogenetic relationship between M. sinensis and M. floridulus , and between M. sacchariflorus and M. lutarioriparius and they cannot be distinguished only based on the ITS sequences.…”

Section: Discussionsupporting

confidence: 84%

“…So far, the phylogenetic relationships among the four Miscanthus species were mainly carried out at the morphological, cellular and molecular levels (Chae et al 2014, Yook et al 2014). In previous studies, the ITS sequence was used to assess the phylogeny of the four Miscanthus species and the species of the Saccharum complex and other related genera (Hodkinson et al 2002b, Chen et al 2007, Liu et al 2010), and the genome relationship between diploid M. sinensis and tetraploid M. sacchariflorus was examined by FISH with rDNA, genomic DNA and Saccharum centromeric repeats (Takahashi and Shibata 2002; Takahashi et al 2002). However, there has been no study on the phylogenetic relationships of all the four species by combining molecular cytogenetic characterization with ITS sequence analysis.…”

Section: Introductionmentioning

confidence: 99%

Molecular cytogenetic characterization and phylogenetic analysis of four Miscanthus species (Poaceae)

Tang¹,

Xiao²,

Iqbal³

et al. 2019

CCG

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Chromosomes of four Miscanthus (Andersson, 1855) species including M. sinensis (Andersson, 1855), M. floridulus (Schumann & Lauterb, 1901), M. sacchariflorus (Hackel, 1882) and M. lutarioriparius (Chen & Renvoize, 2005) were analyzed using sequentially combined PI and DAPI (CPD) staining and fluorescence in situ hybridization (FISH) with 45S rDNA probe. To elucidate the phylogenetic relationship among the four Miscanthus species, the homology of repetitive sequences among the four species was analyzed by comparative genomic in situ hybridization (cGISH). Subsequently four Miscanthus species were clustered based on the internal transcribed spacer (ITS) of 45S rDNA. Molecular cytogenetic karyotypes of the four Miscanthus species were established for the first time using chromosome measurements, fluorochrome bands and 45S rDNA FISH signals, which will provide a cytogenetic tool for the identification of these four species. All the four have the karyotype formula of Miscanthus species, which is 2n = 2x = 38 = 34m(2SAT) + 4sm, and one pair of 45S rDNA sites. The latter were shown as strong red bands by CPD staining. A non-rDNA CPD band emerged in M. floridulus and some blue DAPI bands appeared in M. sinensis and M. floridulus. The hybridization signals of M. floridulus genomic DNA to the chromosomes of M. sinensis and M. lutarioriparius genomic DNA to the chromosomes of M. sacchariflorus were stronger and more evenly distributed than other combinations. Molecular phylogenetic trees showed that M. sinensis and M. floridulus were closest relatives, and M. sacchariflorus and M. lutarioriparius were also closely related. These findings were consistent with the phylogenetic relationships inferred from the cGISH patterns.

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“…Several reports indicated that Erianthus belongs to Saccharum based on the presence/absence of awn whereas this is not exactly. The criteria to differentiate these two genera vary, but recent studies suggested that Saccharum and Erianthus are distinct genera based on various lines of molecular evidence [ 15 – 19 ]. As such, the Saccharum complex is broadly accepted to indicate the relationship between these species.…”

Section: Introductionmentioning

confidence: 99%

An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex)

et al. 2018

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BackgroundSugarcane has recently attracted increased attention for its potential as a source of bioethanol and methane. However, a narrow genetic base has limited germplasm enhancement of sugarcane. Erianthus arundinaceus is an important wild genetic resource that has many excellent traits for improving cultivated sugarcane via wide hybridization. Species-specific repetitive sequences are useful for identifying genome components and investigating chromosome inheritance in noblization between sugarcane and E. arundinaceus. Here, suppression subtractive hybridization (SSH) targeting E. arundinaceus-specific repetitive sequences was performed. The five critical components of the SSH reaction system, including enzyme digestion of genomic DNA (gDNA), adapters, digested gDNA concentrations, primer concentrations, and LA Taq polymerase concentrations, were improved using a stepwise optimization method to establish a SSH system suitable for obtaining E. arundinaceus-specific gDNA fragments.ResultsSpecificity of up to 85.42% was confirmed for the SSH method as measured by reverse dot blot (RDB) of an E. arundinaceus subtractive library. Furthermore, various repetitive sequences were obtained from the E. arundinaceus subtractive library via fluorescence in situ hybridization (FISH), including subtelomeric and centromeric regions. EaCEN2-166F/R and EaSUB1-127F/R primers were then designed as species-specific markers to accurately validate E. arundinaceus authenticity.ConclusionsThis is the first report that E. arundinaceus-specific repetitive sequences were obtained via an improved SSH method. These results suggested that this novel SSH system could facilitate screening of species-specific repetitive sequences for species identification and provide a basis for development of similar applications for other plant species.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1471-6) contains supplementary material, which is available to authorized users.

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Phylogenetic Relationships of Sugarcane Related Genera and Species Based on ITS Sequences of Nuclear Ribosomal DNA

Cited by 4 publications

References 10 publications

Assessment of genetic diversity among different sugarcane genotypes using internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA)

Assessment of genetic diversity among different sugarcane genotypes using internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA)

Molecular cytogenetic characterization and phylogenetic analysis of four Miscanthus species (Poaceae)

An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex)

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