Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

Wang, Rongkai; Fan, Jinshuan; Pan, Chaoyun; Zhu, Ling; Zhao, Ming; Li, Lingli

doi:10.3390/f10020087

Cited by 27 publications

(16 citation statements)

References 33 publications

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“…Simple sequence repeat (SSR) markers are powerful, effective, and economical for the assessment of co-dominant inheritance, with good reproducibility [21,22]. The development of next generation sequencing (NGS) techniques has resulted in a revolution in the field of de novo whole genome assembly and multi-omics of plants [23], and developing genomic or genic SSRs from NGS data is both feasible and affordable [24][25][26].…”

Section: Introductionmentioning

confidence: 99%

Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species

Zheng

Liu

et al. 2021

Forests

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Dalbergia hupeana Hance (D. hupeana) is a precious hardwood tree of the genus Dalbergia. It is one of the few species widely distributed within subtropical areas and is important for timber production and forest restoration. At present, there is little published genetic information on D. hupeana. Therefore, we performed a genome survey using next generation sequencing (NGS) and developed a set of novel genomic SSR (gSSR) markers from the assembled data, and assessed the transferability of these markers to other Dalbergia species in Asia. The results of the genome survey show the genome size of D. hupeana to be about 664 Mb and highly heterozygous. The assembly of sequencing data produced 2,431,997 contigs, and the initial assembly of the NGS data alone resulted in contig N50 of 393 kb with a total of 720 Mb. A total of 127,742 perfect SSR markers were found in the assembled contigs. A total of 37 highly polymorphic and easily genotyped gSSR markers were developed in D. hupeana, while the majority of gSSR markers could be successfully transferred to nine other Dalbergia species in Asia. The transferability rate of gSSR markers was highest in D. balansae, which is more closely related to D. hupeana. Seven gSSR markers were able to be amplified in all tested species. In addition, a preliminary assessment of the genetic diversity of three tree species in the Dalbergia genus suggested a high level of genetic diversity within populations distributed in the subtropical area in China. However, the determination of the global status of their genetic variation still requires further and more comprehensive assessment. Our findings will enable further studies on the genetic diversity, phylogenetics, germplasm characterization, and taxonomy of various Dalbergia species.

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Section: Introductionmentioning

confidence: 99%

Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species

Zheng

Liu

et al. 2021

Forests

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“…Genome surveys, which use next-generation sequencing (NGS), yield a large amount of genomic data in a rapid, cost-effective manner. Genomic data from genome surveys not only provide useful information on genome structure, such as an estimation of genome size, heterozygosity levels, and repeat contents but also establish a genomic sequence resource from which molecular markers can be developed [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Genome survey ofZanthoxylum bungeanumand development of genomic-SSR markers in congeneric species

Kong

et al. 2020

Bioscience Reports

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Zanthoxylum bungeanum, a spice and medicinal plant, is cultivated in many parts of China and some countries in Southeast Asia; however, data on its genome are lacking. In the present study, we performed a whole-genome survey and developed novel genomic-SSR markers of Z. bungeanum. Clean data (∼197.16 Gb) were obtained and assembled into 11185221 scaffolds with an N50 of 183 bp. K-mer analysis revealed that Z. bungeanum has an estimated genome size of 3971.92 Mb, and the GC content, heterozygous rate, and repeat sequence rate are 37.21%, 1.73%, and 86.04%, respectively. These results indicate that the genome of Z. bungeanum is complex. Furthermore, 27153 simple sequence repeat (SSR) loci were identified from 57288 scaffolds with a minimum length > 1 kb. Mononucleotide repeats (19706) were the most abundant type, followed by dinucleotide repeats (5154). The most common motifs were A/T, followed by AT/AT; these SSRs accounted for 71.42% and 11.84% of all repeats, respectively. A total of 21243 non-repeating primer pairs were designed, and 100 were randomly selected and validated by PCR analysis using DNA from 10 Z. bungeanum individuals and 5 Zanthoxylum armatum individuals. Finally, 36 polymorphic SSR markers were developed with polymorphism information content (PIC) values ranging from 0.16 to 0.75. Cluster analysis revealed that Z. bungeanum and Z. armatum could be divided into two major clusters, suggesting that these newly developed SSR markers are useful for genetic diversity and germplasm resource identification in Z. bungeanum and Z. armatum.

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“…The comparative plastome analysis allows detailed insights to affirm the phylogenetic placement of these plants and will be useful for species identification, to verify taxonomic levels and identify phylogenetic relationships [8,18]. Recently, cp genomes of A. miaotaiense and A. truncatum have been reported, but merely the sequence information was provided without further analyses [19,20]. Thus, a comparative study among these two published cp genomes and five newly generated plastomes of sect.…”

Section: Introductionmentioning

confidence: 99%

Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea

Gao

Huang

et al. 2020

Forests

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The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient for the enhancement of the understanding of phylogenetic relationships and taxonomic revision. Here, we report complete cp genomes of five species of Acer sect. Platanoidea. The length of Acer sect. Platanoidea cp genomes ranged from 156,262 bp to 157,349 bp and detected the structural variation in the inverted repeats (IRs) boundaries. By conducting a sliding window analysis, we found that five relatively high variable regions (trnH-psbA, psbN-trnD, psaA-ycf3, petA-psbJ and ndhA intron) had a high potential for developing effective genetic markers. Moreover, with an addition of eight plastomes collected from GenBank, we displayed a robust phylogenetic tree of the Acer sect. Platanoidea, with high resolutions for nearly all identified nodes, suggests a promising opportunity to resolve infrasectional relationships of the most species-rich section Platanoidea of Acer.

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Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

Cited by 27 publications

References 33 publications

Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species

Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species

Genome survey ofZanthoxylum bungeanumand development of genomic-SSR markers in congeneric species

Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea

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