Chloroplast genomes of Lilium lancifolium, L. amabile, L. callosum, and L. philadelphicum: Molecular characterization and their use in phylogenetic analysis in the genus Lilium and other allied genera in the order Liliales (original) (raw)
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Mitochondrial DNA Part B, 2018
Lilium martagon var. pilosiusculum is an endangered species with high ornamental value in Xinjiang province (China). In this study, we reported a complete chloroplast genome of L. martagon var. pilosiusculum, which was de novo assembled using the next-generation sequencing data. The complete chloroplast genome is 152,816 in length, including a large single copy region of 82,265 bp and a small single copy region of 17,541 bp and two inverted repeat regions of 26,505 bp. A total of 110 functional genes were encoded, consisting of 76 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The overall AT content of the chloroplast genome is 63.00%. In addition, 68 SSRs and 31 large repeat sequences were found. In the maximum likelihood tree, a strong phylogenetic signal showed that L. martagon var. pilosiusculum is a species of lilium.
The complete chloroplast genome sequence of Lilium hansonii Leichtlin ex D.D.T.Moore
Mitochondrial DNA, 2015
Lilium hansonii is a lily species native to Korea and an important wild species for lily breeding. The chloroplast genome of L. hansonii was completed by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of L. hansonii was 152 655 bp long and consisted of large single copy region (82 051 bp), small single copy region (17 620 bp) and a pair of inverted repeat regions (26 492 bp). A total of 115 genes were annotated, which included 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that L. hansonii is most closely related to L. superbum (Turk's-cap lily) and L. longiflorum (Easter lily).
The complete chloroplast genome of Lilium davidii var. unicolor (Hoog) cotton (Liliaceae)
Mitochondrial DNA Part B, 2020
Lilium davidii var. unicolor (Hoog) cotton, belonging to the family Liliaceae, has essential medicinal and ornamental values. In this study, the whole chloroplast genome of L. davidii var. unicolor was sequenced for the first time. It has the typical quadripartite circle structure, with a genome size of 152,659 bp. Overall, 110 genes were detected, including 78 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The phylogenetic tree showed that L. davidii var. unicolor was related to L.
PLoS ONE, 2013
Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae) and 155,510bp in Alstroemeria aurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium.
Mitochondrial DNA Part B, 2019
Fritillaria ussuriensis is the important herbal plant in the family Liliaceae, which is used in oriental medicine. In this study, we annotated and analyzed the complete chloroplast genome of F. ussuriensis. The chloroplast genome of F. ussuriensis has a circle structure with 151,478 bp in length and contains a pair of 26,296 bp inverted repeat (IR) regions, which were separated by a large single copy (LSC) region of 81,697 bp and a small single copy (SSC) region of 17,189 bp. The overall nucleotide composition of the complete chloroplast genome is as follows: A of 31.1%, T of 31.9%, C of 18.9%, and G of 18.1%, with a total G รพ C content of the chloroplast genome 37.0%. The complete chloroplast genome of F. ussuriensis encodes total 131 genes, including 85 protein-coding genes (PCGs), 38 transfer RNA genes (tRNAs), and eight ribosome RNA genes (rRNAs). The result of phylogenetic Maximum-Likelihood (ML) tree is set out that shows the closest relationship between F. ussuriensis and Fritillaria karelinii. The complete chloroplast genome provides basic data for further research of genus Fritillaria species useful genome resource in China.
Plants
The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with fi...
Molecular Phylogeny and Genome Size in European Lilies (Genus Lilium, Liliaceae)
Advanced Science Letters, 2010
Several European lilies populations representing 10 species belonging to section Liriotypus and section Martagon were studied for molecular phylogeny (27 populations) and DNA amount (24 populations). Different Lilium sections were easily differentiated by ITS and rpS4-trnT-trnL sequences and genome size assessments, while an extremely low genetic differentiation was detected at a subsectional level. Most of the variability concentrates on polymorphic sites that have not reached fixation, which considerably complicates the selection of an adequate analysis method. Geographical and ecological variations of genome size and ITS sequences within species were noticeable for several Lilium representatives.
Evaluating phylogenetic relationships in the Lilium family using the ITS marker
Journal of Plant Biotechnology
Lilium is a perennial bulbous plant belonging to the liriotypes genus. Our aim was to study the phylogenetic relationships of the Lilium family. Two varieties of Lilium ledebourii, 44 varieties of the gene bank, and one variety from the Tulipa family served as the out group. In order to study the diversity between lilium masses, ITS regions were used to design the marker. The results showed that the guanine base is the most abundant nucleotide. Relatively high conservation was observed in the ITS regions of the populations (0.653). Phylogenetic analysis showed that sargentiae and hybrid varieties are older than other varieties of the Lilium family. Also, the location of L. ledebourii varieties (Damash and Namin) was identified in a phylogenetic tree by using the ITS marker. Overall, our research showed that ITS molecular markers are very suitable for phylogenetic studies in the Lilium family.
Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the
2008
Background: The magnoliids represent the largest basal angiosperm clade with four orders, 19 families and 8,500 species. Although several recent angiosperm molecular phylogenies have supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence has resulted in phylogenies supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. This is one of the most important remaining issues concerning relationships among basal angiosperms. We sequenced the chloroplast genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other completed angiosperm chloroplast genomes to assess phylogenetic relationships among magnoliids. Results: The Drimys and Piper chloroplast genomes are nearly identical in size at 160,606 and 160,624 bp, respectively. The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper). The gene order of both taxa is nearly identical to many other unrearranged angiosperm chloroplast genomes, including Calycanthus, the other published magnoliid genome. Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome. Overall GC content ranges from 34-39%, and coding regions have a substantially higher GC content than non-coding regions (both intergenic spacers and introns). Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd
A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower
2006
Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF , rbcL, as well as non-coding DNA from the trnL intron plus the trnL-trnF intergenic spacer 4], matK [5], and, with lesser resolution, psbA-trnH [6]. This culminated in a study by Panero and Funk in 2002 [1] that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures.