Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: unknown
Published: May 20, 2024
Language: Английский
Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 60(1), P. 1 - 15
Published: Jan. 15, 2021
Abstract Magnoliaceae, an assemblage of early diverged angiosperms, comprises two subfamilies, speciose Magnolioideae with approximately 300 species in varying numbers genera and monogeneric Liriodendroideae Liriodendron L. This family occupies a pivotal phylogenetic position important insights into the diversification shows intercontinentally disjunct distribution patterns between eastern Asia Americas. Widespread morphological homogeneity slow substitution rates Magnolia s.l. resulted poorly supported relationships based on morphology or molecular evidence, which hampers our understanding genus’ temporal spacial evolution. Here, newly generated genome skimming data for 48 species, we produced robust phylogenies using genome‐wide markers from both plastid genomes single nucleotide polymorphism data. Contrasting nuclear revealed extensive cytonuclear conflicts shallow deep relationships. ABBA‐BABA PhyloNet analyses suggested hybridization occurred within sect. Yulania , is concordance ploidy level these sections. Divergence time estimates biogeographic reconstruction indicated that timing three tropical disjunctions coincided mid‐Eocene cooling climate and/or late Eocene deterioration, temperate much later, possibly during warm periods Miocene, hence supporting boreotropical flora concept
Language: Английский
Citations
39
Genes, Journal Year: 2022, Volume and Issue: 13(2), P. 369 - 369
Published: Feb. 18, 2022
, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of
Language: Английский
Citations
25
Plants, Journal Year: 2020, Volume and Issue: 9(2), P. 286 - 286
Published: Feb. 24, 2020
Alpinia katsumadai (A. katsumadai), oxyphylla oxyphylla) and pumila pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification phylogenetic analysis. Here, we sequenced three complete genomes A. katsumadai, sampled from Guangdong pumila, analyzed published zerumbet zerumbet) Hainan retrieve useful molecular resources Alpinia. five possessed typical quadripartite structures comprising large single copy (LSC, 87,248–87,667 bp), small (SSC, 15,306–18,295 bp) pair inverted repeats (IR, 26,917–29,707 bp). They had similar gene contents, orders GC but were slightly different in numbers sequence (SSRs) long repeats. Interestingly, fifteen highly divergent regions (rpl36, ycf1, rps15, rpl22, infA, psbT-psbN, accD-psaI, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, rps11-rpl36, infA-rps8, psbC-psbZ, rpl32-ccsA), could be suitable studies, detected genomes. Comparative analyses among indicated that 1891 mutational events, including 304 nucleotide polymorphisms (SNPs) 118 insertion/deletions (indels) between 367 SNPs 122 indels Guangdong, 331 115 zerumbet, 371 120 Hainan, 20 23 two accessions oxyphylla, accurately located. Additionally, relationships based on SNP matrix 28 whole showed was sister branch Amomum divided into groups, one another other oxyphylla. In conclusion, this study provided genomic further phylogeny Zingiberaceae.
Language: Английский
Citations
36
Plants, Journal Year: 2020, Volume and Issue: 9(4), P. 478 - 478
Published: April 9, 2020
Trifolium L., which belongs to the IR lacking clade (IRLC), is one of largest genera in Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing annotation two annual grasses, alexandrinum (Egyptian clover) T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) insertions/deletions (In/Dels) were discovered between those Global alignment a further thirteen species revealed large amount rearrangement repetitive events these fifteen As hypothetical cp open reading frame (ORF) RNA polymerase subunits, ycf1 rpoC2 genomes both contain vast sequences observed high Pi values (0.7008, 0.3982) resupinatum. Thus they could be considered as candidate genes for phylogenetic analysis In addition, divergence time ranged from 84.8505 Mya 4.7720 Mya. This study will provide insight into evolution
Language: Английский
Citations
33
Life, Journal Year: 2022, Volume and Issue: 12(1), P. 92 - 92
Published: Jan. 9, 2022
Fagus longipetiolata Seemen is a deciduous tree of the genus in Fagaceae, which endemic to China. In this study, we successfully sequenced cp genome F. longipetiolata, compared genomes genus, and reconstructed phylogeny Fagaceae. The results showed that was 158,350 bp, including pair inverted repeat (IRA IRB) regions with length 25,894 bp each, large single-copy (LSC) region 87,671 small (SSC) 18,891 bp. encoded 131 unique genes, 81 protein-coding 37 transfer RNA genes (tRNAs), 8 ribosomal (rRNAs), 5 pseudogenes. addition, 33 codons 258 simple sequence repeats (SSRs) were identified. relatively conserved, especially IR regions, best conservation, no inversions or rearrangements found. five largest variations rps12, rpl32, ccsA, trnW-CCA, rps3 spread over LSC SSC. comparison gene selection pressure indicated purifying main selective pattern maintaining important biological functions genomes. However, ndhD, rpoA, ndhF affected by positive selection. Phylogenetic analysis revealed engleriana formed close relationship, partially overlapped their distribution Our would provide genetic information for further research into classification, evolution Fagus.
Language: Английский
Citations
19
Plant Diversity, Journal Year: 2021, Volume and Issue: 44(1), P. 70 - 82
Published: June 1, 2021
Members of Veratrum are perennial herbs widely used in traditional Chinese medicine to induce vomiting, resolve blood stasis and relieve pain. However, the intrageneric classification phylogenetic relationships within have long been controversial due complexity morphological variations lack high-resolution molecular markers. In this study, we reevaluated infrageneric with genus using complete chloroplast genome sequence data. Herein, cp genomes ten species were newly sequenced characterized. The had typical quadripartite structure, ranging from 151,597 bp 153,711 size comprising a total 135 genes. structure (i.e., gene order, content, components) was highly similar across species. number simple repeats (SSRs) ranged 63 78, 31 35. Eight divergent regions (ndhF, psbC-psbZ, psbK-psbI, rpoB-trnC_GCA, trnK_UUU-trnQ_UUG, trnS_GCU-trnG_UCC, trnT_UGU-trnL_UAA ycf1) identified potentially useful for DNA barcoding Veratrum. Phylogenetic analysis among 29 taxa based on genomes, genes, protein-coding genes intergenic strongly supported monophyly circumscription well-presented great resolution. These results will facilitate identification, taxonomy, utilization plants as well evolutionary studies Melanthiaceae.
Language: Английский
Citations
27
Forests, Journal Year: 2021, Volume and Issue: 12(4), P. 441 - 441
Published: April 6, 2021
Clethra fargesii, an essential ecological and endemic woody plant of the genus in Clethraceae, is widely distributed Central China. So far, there have been a paucity studies on its chloroplast genome. In present study, we sequenced assembled complete genome C. fargesii. We also analyzed features compared them to delavayi other closely related species Ericales. The 157,486 bp length, including large single-copy (LSC) region 87,034 small (SSC) 18,492 bp, separated by pair inverted repeat (IR) regions 25,980 bp. GC content whole 37.3%, while those LSC, SSC, IR are 35.4%, 30.7%, 43.0%, respectively. fargesii encodes 132 genes total, 87 protein-coding (PCGs), 37 tRNA genes, eight rRNA genes. A total 26,407 codons 73 SSRs were identified Additionally, postulated demonstrated that structure may evolutionary conservation based comparative analysis alignment among Ericales species. low Pi values revealed nucleotide diversity two selection pressure was shown few positively selected adaptive evolution using 80 coding sequences (CDSs) genomes phylogenetic tree showed Clethraceae Ericaceae sister clades, which reconfirm previous hypothesis highly conserved 75 CDSs 40 information results presented this study valuable for further intraspecies identification, biogeographic analysis, relationship Clethraceae.
Language: Английский
Citations
27
Gene, Journal Year: 2020, Volume and Issue: 736, P. 144410 - 144410
Published: Jan. 30, 2020
Language: Английский
Citations
22
Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12
Published: July 27, 2021
The genus Pennisetum (Poaceae) is both a forage crop and staple food in the tropics. In this study, we obtained chloroplast genome sequences of four species ( P. alopecuroides , clandestinum glaucum polystachion ) using Illumina sequencing. These genomes have circular structures 136,346–138,119 bp, including large single-copy region (LSC, 79,380–81,186 bp), small (SSC, 12,212–12,409 pair inverted repeat regions (IRs, 22,284–22,372 bp). overall GC content these was 38.6–38.7%. complete contained 110 different genes, 76 protein-coding 30 transfer RNA (tRNA) ribosomal (rRNA) genes. Comparative analysis nucleotide variability identified nine intergenic spacer psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL rpl32-trnL ), which may be used as potential DNA barcodes future identification evolutionary . phylogenetic revealed close relationship between followed by completed study will help facilitate research on relationships evolution species.
Language: Английский
Citations
19
Journal of Applied Genetics, Journal Year: 2023, Volume and Issue: 64(3), P. 419 - 429
Published: June 28, 2023
Language: Английский
Citations
7