- Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae). - Our dating analysis suggested that Lagerstroemia originated in the late Paleocene. - 60 Ma) and started to diversify in the middle Miocene. - Four variable loci, trnD- trnY-trnE, rrn16-trnI, ndhF-rpl32-trnL and ycf1, were discovered in the Lagerstroemia chloroplast genomes.. - utilization of Lagerstroemia.. - There are at least 500 named crape myrtle cultivars avail- able in the U.S., Europe, and Asia [4].. - After detailed analyses of the morphological characters and lit- erature, De Wilde and Duyfjes [5] considered that four sections should be divided in Lagerstroemia: (1) L. - the bark of the trunk, and the length of stamens. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - Full list of author information is available at the end of the article. - There are 115 Lagerstroemia name records in the Plant List database (http://www.theplantlist.org. - and half of the taxonomic status of the name remains unresolved.. - The phylo- genic relationships within Lagerstroemia have been poorly defined overall using several chloroplast markers and/or the ITS and gene regions of the ubiquitin- proteasome system [10, 11]. - The poor phylogenetic reso- lution in previous studies resulted from limited amounts of DNA sequence data available and the low genetic variation in the chosen molecular markers, likely due to this group’s recent origin and rapid radiation.. - In this study, we se- quenced 20 chloroplast genomes of Lagerstroemia sam- ples using next-generation sequencing (NGS). - Characteristics of Lagerstroemia chloroplast genomes The complete chloroplast genomes of the 20 newly se- quenced Lagerstroemia species ranged in length from 151,968 bp (L. - speciosa) and accounted for of the total length. - 03) and accounted for of the total length. - 16.91 % of the total length. - A total of 112 unique genes were detected in the chloroplast genomes of the 20 Lagerstroemia species, including 78 coding genes, 30 tRNA genes and 4 rRNA genes (Fig. - The alignment matrix of the chloroplast genome was 154,185 bp. - 1 General chloroplast genome map of Lagerstroemia. - Genes drawn outside of the map circle are transcribed clockwise, while those drawn inside are transcribed counterclockwise. - The darker gray in the inner circle corresponds to GC, while the lighter gray corresponds to AT content. - 0.02), including trnD-trnY- trnE, rrn16-trnI, ndhF-rpl32-trnL and ycf1, were detected in the Lagerstroemia chloroplast genomes (Fig. - Among these regions, trnD-trnY-trnE was located in the LSC region, rrn16-trnI was located in the IR region, and ndhF-rpl32-trnL and ycf1 were located in the SSC re- gion. - The number of variable sites of the four markers ranged from 38 (trnD-trnY- trnE) to 56 (rrn16-trnI and ndhF-rpl32-trnL), whereas the universal DNA barcodes had lower divergence. - The average nucleotide diversity of the four rapidly evolving regions was 0.01941, which was 2.5 times higher than that of the universal DNA barcodes. - Characteristics of the six different datasets used in this study are shown in Table 3. - Dataset-1 and Dataset-2 strongly supported the monophyly of Lagerstroemia (BS = 100/PP = 1.0). - In this study, analyses based on each dataset revealed four clades in the genus Lagerstroemia. - glabra formed a clade and showed short branch in the trees. - The topology of the Lager- stroemia samples with high resolution was achieved based on the whole chloroplast genome sequence data (Fig. - Figures S2, S3, and S4 show the general decrease in resolution capacity of the topology when either the LSC, IR, or SSC region was used due to the insufficient information.. - Different fossil calibration combinations were computed to investigate the variation of estimation values of the di- vergence times (Table 4). - According to the fossil records, Lagerstroemia first ap- peared in the late Paleocene/early Eocene of the Indian subcontinent [18]. - The stem node of the Lagerstroemia was dated to 60.12 Ma (95 % highest posterior density, HPD: 56.2. - 2 Sliding window analysis of nucleotide variability (Pi) across 35 complete chloroplast genome sequences of Lagerstroemia. - the crown node of the Lagerstroemia was dated to 31.6 Ma (95 %HPD Ma). - Our results indicate that the mutation patterns of the chloroplast genomes were not uniform. - In general, mutation hotspots are rare in the IR region. - The ycf1 locus was the most divergent marker in the Lagerstroemia chloroplast genome (Fig. - Table 3 Characteristics of the six different data sets. - 2 Complete chloroplast genome sequences (deletion some sites according to the outgroups. - 3 Complete chloroplast genome sequences . - Phylogenetics of Lagerstroemia. - De Wilde and Duyfjes [5] classified Lager- stroemia into four sections on the basis of the mono- graph by Furtado &. - Several morphological features used for morphological classification of Lager- stroemia in previous reports, such as (1) the number of the ridges on the calyx tube, (2) the number of the ridges is the same as or twice the number of sepals, and (3) glabrous or hairy within the calyx lobes, may be ob- served in the same clade generated based on the molecu- lar classification. - venusta is the same as the sepal number, but each of the other two taxa (L. - However, the genetic background of the cultivars was unclear, and these markers were not informative to infer the relationship of those species. - In this study, we recovered a well-supported and species-level relationship of Lagerstroemia using six dif- ferent chloroplast genome datasets. - However, the four clade classifications were different from the morphological classification of the genus [1].. - glabra were in the section Adambea, the molecular results showed L.. - speciosa was in the clade 1, L. - limii in the clade 3, and L.. - glabra in the clade 4, respectively.. - 3 Molecular phylogeny of Lagerstroemia from ML (maximum likelihood) and BI (Bayesian inference) analyses using different data sets. - the chloroplast genome sequences (dataset-2). - However, the relation- ship of Lagerstroemia was inconsistent with this study.. - intermedia [17] which affected the topology of the phylogenetic tree. - Divergence time of Lagerstroemia. - The fossil record of the Lagerstroemia consists of leaf impressions, wood, and pollen [18]. - According to the fossil record, the oldest confirmed evidence of the Lager- stroemia is a leaf impression of L. - Those records indicated the origin time of Lagerstroemia was earlier than 56 Ma.. - There were a number of putative fossil Lagerstroemia leaves and wood in the middle Miocene [18]. - Those fossil records suggest that Lagerstroemia was common and somewhat diverse in the wet subtropical forests of the Indian subcontinent in the middle Miocene. - 4 Molecular phylogeny of Lagerstroemia resulting from ML and BI analyses using whole chloroplast genome sequences (dataset-3).. - Diversifi- cation with Lagerstroemia occurred in the Pleistocene ~ 5.3 Ma, and at this time, this genus is present and per- sists in Japan [18, 41].. - In this study, we report 20 newly sequenced chloroplast genomes of the genus Lagerstroemia. - The relationship and divergence times of Lagerstroemia were revealed using complete chloroplast genome sequence data. - In order to infer the framework of the phylogenetic relationship, we sampled 20 individuals of 17 described species, which represented all the four sec- tions and six of eight subsections. - The materials were obtained from the field, botanical gardens and the herb- arium of the Institute of Botany, Chinese Academy of Sciences (PE, Table S1). - Three crape myrtle samples could not be accurately identified morphologically be- cause of the lack of morphological characters. - In addition to the newly collected material for DNA se- quencing, publicly available complete chloroplast gen- ome sequences (15 accessions, Table S1) of Lagerstroemia were also included in this analysis.. - subcostata chloroplast genome sequence as a reference (GenBank accession number: KF572029). - Physical maps of the circular chloroplast ge- nomes were visualized with OGDRAW [46]. - To access the phylogenetic effects of the different re- gions in the chloroplast genome, we created six datasets based on different chloroplast genome regions or using different outgroups. - Dataset-2 included 35 whole chloroplast genome sequences of Lagerstroemia and five other species of Lythraceae as outgroups (Lythrum salicaria, Lawsonia inermis, Rotala rotundifo- lia, Sonneratia alba, and Duabanga grandiflora). - This fossilized pollen was used to offset for the crown of the two lineages. - The oldest confirmed fossil of Lagerstroemia patelii Lakhanpal &. - Each of the five fossil priors (Lythrum elkensis/Peplis eaglensis, Son- neratiaoxylon preapetalum, Punicoxylon eocenicum, Lawsonia lawsonioides, and Lagerstroemia patelii) was given a lognormal distribution with offset values as spe- cified (i.e and 56.0 Ma,. - Taxa included in the present study.. - Molecular phylogeny of Lagerstroemia resulting from ML (maximum likelihood) and BI (Bayesian inference) analyses using LSC regions (dataset-4). - Molecular phylogeny of Lagerstroemia resulting from ML (maximum likelihood) and BI (Bayesian inference) analyses using IR regions (dataset-5). - Molecular phylogeny of Lagerstroemia resulting from ML (maximum likelihood) and BI (Bayesian inference) analyses using SSC regions (dataset-6). - The authors thank Boxing Hou, Cuihua Gu, Xiaobai Jin, Jin Chen, Shouzhou Zhang, Jun-jie Yu, Zulin Ning, Bingqiang Xu, Huijin Zhang, Kaihong He, Zhir- ong Yang, and Ruili Li for their advice and kind help in the field investigation and sample collection. - The authors thank the Plant DNA Bank of China in the Institute of Botany, Chinese Academy of Sciences for providing materials.. - The chloroplast genome of Lagerstroemia under study is deposited in the GenBank database under the following accession numbers: MT019844 - MT019863. - A revision of Lagerstroemia L.(Lythraceae). - Survey of Lagerstroemia L. - Phylogenetic analysis of the Sonneratiaceae and its relationship to Lythraceae based on ITS sequences of nrDNA. - Phylogenetic analysis of the Lythraceae based on four gene regions and morphology. - Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae. - Fossil records in the Lythraceae. - Plastid genome evolution in the early-diverging Legume subfamily Cercidoideae (Fabaceae). - Floristics and climate during Siwalik (Middle Miocene) near Kathgodam in the Himalayan foot-hills of Uttranchal, India. - Plant remains from the Tipam sandstones of northeast India with remarks on the palaeoecology of the region during the Miocene. - Comparison of the Tertiary flora of southwest China and northeast India and its significance in the antiquity of the modern Himalayan flora. - A plant macrofossil assemblage from the Kiyokawa Formation in the Shimousa Group and reconstruction of the palaeoclimate based on it
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt