Characterization of the Complete Chloroplast Genomes and Phylogenetic Analysis of Sapotaceae DOI Creative Commons

Wenyan He,

Yumei Liu, Rui Gao

et al.

Horticulturae, Journal Year: 2024, Volume and Issue: 10(12), P. 1375 - 1375

Published: Dec. 20, 2024

The Sapotaceae family comprises 65–70 genera and over 1250 species, holding significant ecological economic value. Although previous studies have made some progress in the phylogenetic relationships classification of Sapotaceae, many issues remain unresolved require further in-depth research. In this study, we sequenced assembled complete chloroplast genomes 21 plants from 11 conducted a comparative genomic analysis, performed analysis by incorporating 16 previously published Sapotaceae. results showed that genome sizes range between 157,920 bp 160,130 bp, exhibiting typical quadripartite structure. Each contains 84–85 protein-coding genes, 37 tRNA 8 rRNA while ndhF gene is absent Pouteria campechiana sapota. relative synonymous codon usage (RSCU) isoleucine (Ile) most commonly used, for methionine (Met) least utilized. Additionally, five highly variable regions (petA-psbJ, psbI-trnS-GGA, rpl2_2-psbA, rps19-rpl2_2, ycf4-cemA) two coding sequences, ycf1 matK, were identified as candidate molecular markers species differentiation within family. Phylogenetic trees reconstructed using sequences analyzed ML BI methods, which revealed divided into three distinct clades, each receiving strong statistical support (BS = 100, PP 1). intergeneric Madhuca Palaquium are sister groups 91, 1), Gambeya Chrysophyllum among larger but traditional boundaries these unstable unfeasible, current genus fail to their natural evolutionary relationships. tree, Eberhardtia aurata placed on separate branch. morphological system shows E. has rust-colored pubescence its branches, abaxial leaf surfaces, petioles, other areas, clearly distinguishes it genera. This study provides valuable insights advancing research, population genetics, breeding, conservation strategies comparing structures characteristics constructing trees.

Language: Английский

De Novo Transcriptome Assembly, Novel EST-SSR Development, and Preliminary Genetic Analysis in Saussurea costus (Falc.) Lipsch, an Industrially Important Endangered Medicinal Herb of the North-Western Himalayas DOI

Kamal Thakur,

Rajnish Sharma, Parul Sharma

et al.

Plant Molecular Biology Reporter, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 4, 2025

Language: Английский

Citations

0
The First Genome-Wide Survey Analysis of the Tibetan Plateau Tetraploid Schizothorax curvilabiatus Reveals Its Microsatellite Characteristics and Phylogenetic Relationships DOI Open Access
Bingjian Liu,

Lizhi Gao,

Y Liu

et al.

Genes, Journal Year: 2025, Volume and Issue: 16(5), P. 491 - 491

Published: April 25, 2025

Background/Objectives: Schizothorax curvilabiatus, a typical highland polyploid species within the subfamily Schizothoracinae, holds economic value and ecological research significance. Currently, there are no related genomic studies. To obtain its genetic information lay foundation for subsequent whole-genome map construction, this study conducted genome survey analysis, preliminary assembly, microsatellite identification, repeat sequence annotation, mitochondrial characterization, phylogenetic relationship research. Methods: DNA was sequenced on DNBSEQ-T7 platform to paired-end data. The analyzed using GCE, draft assembled with SOAPdenovo. Microsatellites were identified MISA, NOVOPlasty. Genome features analyzed, trees constructed PhyloSuite MEGA. Results: size estimated at 2.53 Gb, heterozygosity of 6.55% 47.66% sequences. A 1.324 Gb obtained, sequences comprising 47.17%, majority being transposons (24.64%). Dinucleotide repeats most abundant (46.91%), followed by mononucleotide (38.31%), A/T AC/GT frequent. complete 16,589 bp assembled, 939 D-loop annotated. Phylogenetic relationships among genera in Schizothoracinae also clarified. Conclusions: This provides latest molecular data analysis S. curvilabiatus populations, first time offers resources adaptive evolution polyploidization high-altitude environments.

Language: Английский

Citations

0
Development of Roselle (Hibiscus sabdariffa L.) Transcriptome-Based Simple Sequence Repeat Markers and Their Application in Roselle DOI Creative Commons

Aifen Tao,

Yun-Qing Li,

J. Chen

et al.

Plants, Journal Year: 2024, Volume and Issue: 13(24), P. 3517 - 3517

Published: Dec. 16, 2024

Roselle (Hibiscus sabdariffa L.) simple sequence repeat (SSR) markers were developed using RNA sequencing technology, providing a foundation for genetic analysis and the identification of roselle varieties. In this study, 10 785 unigenes containing 12 994 SSR loci with an average one locus per 6.87 Kb identified, occurrence frequency was 11.36%. Trinucleotide motifs most abundant, followed by dinucleotide repeats, AAG/CTT AT/AT being predominant types, respectively. After screening 100 primer pairs polymorphic ratio 32.0%, we obtained 32 pairs, resulting in clear stable bands. Twenty-seven highly or moderately polymorphic, seven polymorphic. Genetic relationship based on selected primers showed that 38 accessions classified into different clades, those from same regions clustered subgroups. contrast, individuals unique morphological traits separated. DNA fingerprints varieties constructed five primers, effective method identifying at molecular level. Our data provide novel insights genetics H. may be used SSR-assisted breeding.

Language: Английский

Citations

0
Assessing Genetic Diversity in Endangered Plant Orchidantha chinensis: Chloroplast Genome Assembly and Simple Sequence Repeat Marker-Based Evaluation DOI Open Access
Yiwei Zhou, Jianjun Tan, Lishan Huang

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(20), P. 11137 - 11137

Published: Oct. 17, 2024

Orchidantha chinensis T. L. Wu, an endemic species in China, is listed as a key protected wild plant Guangdong Province. However, the lack of reports on chloroplast genome and simple sequence repeat (SSR) markers has hindered assessment its genetic diversity conservation strategies. The limited number molecular to assess this species, thus develop proper strategies, highlighted urgent need new ones. This study developed SSR investigated variation using 96 samples O. from seven populations. Through high-throughput sequencing, complete 134,407 bp was assembled. A maximum-likelihood phylogenetic tree, based genome, showed that closely related Ravenala madagascariensis. identified 52 SSRs (cpSSRs) 5094 expressed tag (EST-SSRs) loci leaf transcriptome, respectively. Twenty-one polymorphic (seven cpSSRs fourteen EST-SSRs) were selected evaluate accessions across Among these markers, one cpSSR 11 EST-SSRs had high polymorphism information content (>0.5). Cluster, principal coordinate, structure analyses indicated groups G1 G6 distinct other five groups. analysis variance greater within than among distance populations significantly positively correlated with geographical distance. These findings provide for studying variability offer theoretical foundation

Language: Английский

Citations

0
Characterization of the Complete Chloroplast Genomes and Phylogenetic Analysis of Sapotaceae DOI Creative Commons

Wenyan He,

Yumei Liu, Rui Gao

et al.

Horticulturae, Journal Year: 2024, Volume and Issue: 10(12), P. 1375 - 1375

Published: Dec. 20, 2024

The Sapotaceae family comprises 65–70 genera and over 1250 species, holding significant ecological economic value. Although previous studies have made some progress in the phylogenetic relationships classification of Sapotaceae, many issues remain unresolved require further in-depth research. In this study, we sequenced assembled complete chloroplast genomes 21 plants from 11 conducted a comparative genomic analysis, performed analysis by incorporating 16 previously published Sapotaceae. results showed that genome sizes range between 157,920 bp 160,130 bp, exhibiting typical quadripartite structure. Each contains 84–85 protein-coding genes, 37 tRNA 8 rRNA while ndhF gene is absent Pouteria campechiana sapota. relative synonymous codon usage (RSCU) isoleucine (Ile) most commonly used, for methionine (Met) least utilized. Additionally, five highly variable regions (petA-psbJ, psbI-trnS-GGA, rpl2_2-psbA, rps19-rpl2_2, ycf4-cemA) two coding sequences, ycf1 matK, were identified as candidate molecular markers species differentiation within family. Phylogenetic trees reconstructed using sequences analyzed ML BI methods, which revealed divided into three distinct clades, each receiving strong statistical support (BS = 100, PP 1). intergeneric Madhuca Palaquium are sister groups 91, 1), Gambeya Chrysophyllum among larger but traditional boundaries these unstable unfeasible, current genus fail to their natural evolutionary relationships. tree, Eberhardtia aurata placed on separate branch. morphological system shows E. has rust-colored pubescence its branches, abaxial leaf surfaces, petioles, other areas, clearly distinguishes it genera. This study provides valuable insights advancing research, population genetics, breeding, conservation strategies comparing structures characteristics constructing trees.

Language: Английский

Citations

0