Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae)

Saina, Josphat K.; Li, Zhizhong; Mekbib, Yeshitila; Gichira, Andrew W.; Liao, Yi-Ying

doi:10.1007/s11033-020-05402-w

Cited by 9 publications

(7 citation statements)

References 77 publications

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“…We identified 324 SSRs in cp genomes of six Magnoliaceae species, most of which had mononucleotide repeats composed of A/T. These SSRs can be used to develop microsatellite markers for genetic diversity and evolution analyses [ 35 ]. We also screened a total of seven highly variable regions through nucleotide diversity analysis.…”

Section: Discussionmentioning

confidence: 99%

Comparative Chloroplast Genomes of Six Magnoliaceae Species Provide New Insights into Intergeneric Relationships and Phylogeny

Yang

Tian

et al. 2022

Biology

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Magnoliaceae plants are industrial tree species with high ornamental and medicinal value. We published six complete chloroplast genomes of Magnoliaceae by using Illumina sequencing. These showed a typical quadripartite structure of angiosperm and were 159,901–160,008 bp in size. A total of 324 microsatellite loci and six variable intergenic regions (Pi > 0.01) were identified in six genomes. Compared with five other genomes, the contraction and expansion of the IR regions were significantly different in Manglietia grandis. To gain a more thorough understanding of the intergeneric relationships in Magnoliaceae, we also included 31 published chloroplast genomes of close relative species for phylogenetic analyses. New insights into the intergeneric relationships of Magnoliaceae are provided based on our results and previous morphological, phytochemical and anatomical information. We suggest that the genus Yulania should be separated from the genus Michelia and its systematic position of should be restored; the genera Paramichelia and Tsoongiodendron should be merged into the genus Michelia; the genera Pachylarnax and Parakmeria should be combined into one genus. These findings will provide a theoretical basis for adjusting the phylogenetic position of Magnoliaceae at the molecular level.

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Section: Discussionmentioning

confidence: 99%

Comparative Chloroplast Genomes of Six Magnoliaceae Species Provide New Insights into Intergeneric Relationships and Phylogeny

Yang

Tian

et al. 2022

Biology

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“…We identi ed 324 SSRs in cp genomes of six Magnoliaceae, most of which were detected monon-ucleotide repeats were composed of A/T. These SSRs can be used to develop microsatllite markers for genetic diversity and evolution analysis (Saina et al 2021). We also screened a total of 7 highly variable regions by nucleotide diversity analysis.…”

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genomes of six Magnoliaceae species provides new insight into intergeneric relationship and phylogeny

Yang

Tian

et al. 2022

Preprint

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The Magnoliaceae plants are industrial tree species with high medicinal value. We published the 6 complete chloroplast genomes of the family Magnoliaceae by using Illumina sequencing. These 6 chloroplast genomes showed a typical quadripartite structure of angiosperm and were 159,901 − 160,008 bp in size, respectively. A total of 324 microsatellite loci and 6 variable intergenic regions (Pi > 0.01) were identified in 6 genomes. Compare with other 5 genomes, the contraction and expansion of the IR regions were significantly different in Manglietia grandis. For having more thorough understanding of the intergeneric relationship of family Magnoliaceae, we also included 31 published chloroplast genomes of close relative species for phylogenetic analyses. The new insights into intergeneric relationship of family Magnoliaceae was provided based on the combination of our result and the previous morphological, phytochemical and anatomygical information. We suggest that the genus Yulania should be separated from the genus Michelia, and restore systematic position of the genus Yulania; the genera Paramichelia and Tsoongiodendron should be merged into the genera Michelia; the genera Pachylarnax and Parakmeria should be combined into one genus. These findings will provide a theoretical basis for adjustment phylogenetic position of family Magnoliaceae at the molecular level.

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“…The methods for cDNA library construction for Illumina sequencing followed Saina et al (2021) . The library was sequenced by Illumina HiSeq 2500 sequencing platform and paired-end reads were generated.…”

Section: Methodsmentioning

confidence: 99%

“…The library was sequenced by Illumina HiSeq 2500 sequencing platform and paired-end reads were generated. High-quality clean reads were produced from roughly 5GB raw data and the transcriptome assembly of Sagittaria trifolia was performed in Trinity program ( Saina et al, 2021 ). For each gene, the longest transcript was selected as unigenes after assembly.…”

Section: Methodsmentioning

confidence: 99%

De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn

Tang

Saina

Long³

et al. 2022

PeerJ

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Background Sagittaria trifolia Linn. is a widespread macrophyte in Asia and southeast Europe and cultivated in parts of Asia. Although a few genomic studies have been conducted for S. trifolia var. sinensis, a crop breed, there is limited genomic information on the wild species of S. trifolia. Effective microsatellite markers are also lacking. Objective To assemble transcriptome sequence and develop effective EST-SSR markers for S. trifolia. Methods Here we developed microsatellite markers based on tri-, tetra-, penta-, and hexa-nucleotide repeat sequences by comparatively screening multiple transcriptome sequences of eleven individuals from ten natural populations of S. trifolia. Results A total of 107,022 unigenes were de novo assembled, with a mean length of 730 bp and an N50 length of 1,378 bp. The main repeat types were mononucleotide, trinucleotide, and dinucleotide, accounting for 55.83%, 23.51%, and 17.56% of the total repeats, respectively. A total of 86 microsatellite loci were identified with repeats of tri-, tetra-, penta-, and hexa-nucleotide. For SSR verification, 28 polymorphic loci from 41 randomly picked markers were found to produce stable and polymorphic bands, with the number of alleles per locus ranging from 2 to 11 and a mean of 5.2. The range of polymorphic information content (PIC) of each SSR locus varied from 0.25 to 0.80, with an average of 0.58. The expected heterozygosity ranged from 0.29 to 0.82, whereas the observed heterozygosity ranged from 0.25 to 0.90. Conclusion The assembled transcriptome and annotated unigenes of S. trifolia provide a basis for future studies on gene functions, pathways, and molecular mechanisms associated with this species and other related. The newly developed EST-SSR markers could be effective in examining population genetic structure, differentiation, and parentage analyses in ecological and evolutionary studies of S. trifolia.

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Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae)

Cited by 9 publications

References 77 publications

Comparative Chloroplast Genomes of Six Magnoliaceae Species Provide New Insights into Intergeneric Relationships and Phylogeny

Comparative Chloroplast Genomes of Six Magnoliaceae Species Provide New Insights into Intergeneric Relationships and Phylogeny

Comparative chloroplast genomes of six Magnoliaceae species provides new insight into intergeneric relationship and phylogeny

De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn

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