Mining and characterization of novel EST-SSR markers of Parrotia subaequalis (Hamamelidaceae) from the first Illumina-based transcriptome datasets

Zhang, Yunyan; Zhang, Mengyuan; Hu, Yimin; Zhuang, Xin; Xu, Wuqin; Li, Pengfu; Wang, Zhongsheng

doi:10.1371/journal.pone.0215874

Cited by 11 publications

(9 citation statements)

References 47 publications

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“…The distribution of motif types varies among plants. The most frequent motif type for Parrotia subaequalis was Di- [39], while the most frequent motif type for Lychnis kiusiana and Dendrocalamus hamiltonii was Tri- [40,41]. In this study, Di-repeats were the most abundant motif (mononucleotides were not considered) in P. lactiflora, and AG/CT accounted for 36.55% of all SSRs, followed by AT/AT (14.78%) and AC/GT (11.97%).…”

Section: Discussionmentioning

confidence: 56%

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

Wan

Zhang

Hong³

et al. 2020

Genes

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The insufficient number of available simple sequence repeats (SSRs) inhibits genetic research on and molecular breeding of Paeonia lactiflora, a flowering crop with great economic value. The objective of this study was to develop SSRs for P. lactiflora with Illumina RNA sequencing and assess the role of SSRs in gene regulation. The results showed that dinucleotides with AG/CT repeats were the most abundant type of repeat motif in P. lactiflora and were preferentially distributed in untranslated regions. Significant differences in SSR size were observed among motif types and locations. A large number of unigenes containing SSRs participated in catalytic activity, metabolic processes and cellular processes, and 28.16% of all transcription factors and 21.74% of hub genes for inflorescence stem straightness were found to contain SSRs. Successful amplification was achieved with 89.05% of 960 pairs of SSR primers, 55.83% of which were polymorphic, and most of the 46 tested primers had a high level of transferability to the genus Paeonia. Principal component and cluster dendrogram analyses produced results consistent with known genealogical relationships. This study provides a set of SSRs with abundant information for future accession identification, marker-trait association and molecular assisted breeding in P. lactiflora.

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Section: Discussionmentioning

confidence: 56%

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

Wan

Zhang

Hong³

et al. 2020

Genes

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“…However, the downstream development and identification of usable and researchable polymorphic SSRs is still a manual and time-consuming process [39]. Recently, an integrated procedure called CandiSSR was developed and used to obtain polymorphic SSRs in silico using genomic or transcriptomic sequence data [40]. In the present study, using the bioinformatics pipeline, we identified 811 potential polymorphic SSRs in six sequenced transcriptomes of T. mongolica.…”

Section: Identifying and General Profiling Of Genic Ssrs In T Mongolmentioning

confidence: 96%

“…By comparing our finding with some other SSR development projects performed using CandiSSR, we found a similar polymorphic genic SSRs generation rate among these different studies. For example, 497 polymorphic genic SSRs were identified in the comparison of the transcriptomes representing the northern and southern population of Parrotia subaequalis [40]; and 1663 polymorphic EST-SSRs were identified by comparing the transcriptomes of tea plant and 19 Camellia species [48]. The identified SSRs in these studies were relatively small.…”

Section: Identifying and General Profiling Of Genic Ssrs In T Mongolmentioning

confidence: 98%

“…CandiSSR was used to identify potential polymorphic genic SSRs among the six unigenes datasets of T. mongolica [39]. The parameters used in the pipeline were: flanking sequence length 100 bp, blast e-value cutoff 1.0 × e −10 , blast identity cutoff 95%, and blast coverage cutoff 95% [39,40]. The SSR search criteria were designed for di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, with a minimum repeat number of six, five, five, four, and four, respectively, while SSRs with mono-nucleotide repeats and motif bigger than six nucleotides were not examined in this study.…”

Section: Identification Of Potential Polymorphic Genic Ssrsmentioning

confidence: 99%

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Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

Dang

Huang

Jia

et al. 2020

Genes

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Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in genes, and identified 811 polymorphic SSRs. Of the identified SSRs, 172, 470, and 76 were located in 5 UTRs, CDSs, and 3 UTRs in 591 transcripts; and AG/CT, AAC/GTT, and AT/AT were the most abundant repeats in each gene region. Functional annotation showed that many of the identified polymorphic SSRs were in genes that were enriched in several GO terms and KEGG pathways, suggesting the functional significance of these genes in the environmental adaptation process. The identification of polymorphic genic SSRs in our study lays a foundation for future studies investigating the contribution of SSRs to regulation of genes in natural populations of T. mongolica and their importance for adaptive evolution of this species.Genes 2020, 11, 322 2 of 13 is a good candidate for studies of plant origin, evolution, and adversity adaptation in such desert regions. Around these topics, a series of fundamental research investigations have been implemented, the results of which are of importance for comprehensively understanding the properties of T. mongolica. This pioneering work includes the studies of systematic, geographic, and taxonomic aspects [7-9]; morphology and anatomy [10][11][12]; physiological ecology [13][14][15][16]; chemometrics and biochemistry [17,18]; population genetics [5]; conservation biology [19][20][21]; abiotic stress response [3]; and medicinal phytochemistry [22,23]. In recent decades, the plant has suffered from serious habitat destruction in size and has even disappeared, leading to the general decline of the species and making the survival of T. mongolica much harder than before [24]. Correspondingly, one consideration for the ongoing survival of the species that has been paid much attention recently is an apparent decrease in genetic diversity due to loss of demographics, inbreeding depression, stochastic events, and other factors [5,24]. However, contrary to the assumption of diversity loss, it has been observed that the species has an intermediate or high level of genetic diversity as detected from analyses of inter-simple sequence repeats and nuclear microsatellites, respectively [5,24]. Therefore, further exploration of these hereditary characteristics and a potential link to adaptation strategies of the species is needed.Genic simple sequence repeats (SSRs) (also called genic microsatellites or expressed sequence tag (EST)-SSRs), a relatively newly established concept, are simple sequence repeats located in ...

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“…P. subaequalis is of great value in a variety of aspects. First, this species is a relict living-fossil plant originating from the Tertiary, which may play a significant role in reflecting the phylogeny of Hamamelidaceae (Hao et al 1996;Zhang et al 2019) and the origin of early angiosperms (Li and Tredici 2008;Zhang et al 2021). Second, P. subaequalis yields good timber with fine wood-grain, being hard and heavy (Zhong 2016).…”

Section: Introductionmentioning

confidence: 99%

Structural diversity and conservation implications of Parrotia subaequalis (Hamamelidaceae), a rare and endangered tree species in China

Liu¹,

Zhang²,

Xue³

2021

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Parrotia subaequalis (H. T. Chang) R.M. Hao & H.T. Wei is a rare and endangered Tertiary relict tree that is endemic to subtropical China. However, little is known about its growth condition and relationship with associated tree species. Here, for the first time we measured the structural diversity of P. subaequalis communities at three representative sites in eastern China using four structural indices, including mingling, tree-tree distance, and diameter and tree height differences. The results showed that: 1) Collectively, most P. subaequalis and associated tree species were small and mid-sized classes in tree height, and small-sized class in diameter; 2) There were two or more other tree species around most of P. subaequalis individuals across the three sites; 3) Overall, the mean distance between reference trees and their neighbors was mainly 1–2 m. Our results indicated that a strong interspecific competition existed between P. subaequalis and its associated tree species. Meanwhile, although the reference tree P. subaequalis had slight advantages in both horizontal and vertical planes, we think that it is necessary to take some effective measures to reduce the interspecific competition and thereby keep it at a proper successive stage. In addition, we also discuss the protection level of P. subaequalis in China, and propose to keep this species at the First-Grade State Protection.

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Mining and characterization of novel EST-SSR markers of Parrotia subaequalis (Hamamelidaceae) from the first Illumina-based transcriptome datasets

Cited by 11 publications

References 47 publications

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

Structural diversity and conservation implications of Parrotia subaequalis (Hamamelidaceae), a rare and endangered tree species in China

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