ABSTRACT
Dendrocalamus liboensis Hsueh & D. Z. Li 1985 is a unique member of the Bambusoideae subfamily found in Guizhou, China. The species has both economic importance and ornamental value. This study represents the first report of the sequencing and assembly of the complete chloroplast genome of D. liboensis. The total length of the genome was 139,483 bp, with a conventional quadripartite framework consisting of a large single-copy (LSC) region (83,001 bp in length), a small single-copy (SSC) region (12,896 bp in length), and two inverted repeats (IR) regions (both 21,793 bp in length). Overall, the D. liboensis chloroplast genome contained 128 functional genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis showed that D. liboensis closely resembled D. sapidus, with both found on a strongly supported branch of the phylogenetic tree.
ABSTRACT
Chimonobambusa utilis (Keng) Keng F is an endemic species distributed only in the Daluoshan Mountains, southwest China. Ch. utilis is popular due to its unique flavor and deliciousness and plays an important role in the industrial revolution in many counties in China. A total of 20 natural populations were sampled from the entire distribution range of Ch. utilis. In the present study, we used five EST-SSR molecular markers, three chloroplast DNA (trnH-psbA, atpF-atpH, and psbK-psbI), and one ITS molecular marker to elucidate the genetic diversity and phylogeography analyses of these Ch. utilis populations. The results exhibited that Ch. utilis populations showed lower genetic diversity than other angiosperms (HT = 0.752, HS = 0.364, and FST = 0.05021 for EST-SSR; HT = 0.956, Hs = 0.507, and FST = 0.70121 for cpDNA; HT = 0.868, Hs = 0.495, and FST = 0.70121 for nrDNA). A total of 40 alleles were detected for five polymorphic loci. We detected 20 polymorphic sites and 11 haplotypes within 1,398 bp of cpDNA and 59 polymorphic sites and 32 haplotypes within the 589 bp of the ITS sequence. Based on the haplotype distribution, we infer that there were at least two glacial refuges of Ch. utilis populations during the Quaternary Ice Age. The genetic and geographic distance were correlated (p < 0.05), indicating that narrow distribution might be the primary cause of the low genetic differentiation of Ch. utilis populations. Based on the genetic diversity of Ch. utilis populations, we recommend implementing effective genetic resource management and sustainable utilization.
ABSTRACT
Chimonobambusa luzhiensis (Poaceae: Bambusoideae) is an endangered plant endemic to Guizhou Province, China. Here, we report the complete chloroplast genome of C. luzhiensis. The plastid genome revealed a typical quadripartite structure with a length of 139,896 bp, including a large single-copy (LSC, 83,191 bp) region, a small single-copy (SSC, 12,811 bp) region, and a pair of inverted repeat (IR) regions (IRa and IRb, 21,797 bp). A total of 131 genes, including 86 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes were annotated, and the overall GC content was 38.8%. Phylogenetic analysis showed that the relationship between C. luzhiensis is sister to C. tumidisinoda.
ABSTRACT
Chimonobambusa hirtinoda, a threatened species, is only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used to obtain the complete chloroplast (cp) genome sequence of C. hirtinoda. The sequence was assembled and analyzed for phylogenetic and evolutionary studies. Additionally, we compared the cp genome of C. hirtinoda with previously published Chimonobambusa species. The cp genome of C. hirtinoda has a total length of 139, 561 bp and 38.90% GC content. This genome included a large single -copy (LSC) region of 83, 166 bp, a small single-copy (SSC) region of 20, 811 bp and a pair of inverted repeats of 21,792 bp each. We discovered 130 genes in the cp genome, including 85 protein-coding genes, 37 tRNA, and 8 rRNA genes. A total of 48 simple sequence repeats (SSRs) were detected. The A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained by measuring the codon usage frequency of amino acids. Furthermore, phylogenetic analysis using complete cp sequences and matK gene revealed a genetic relationship within the Chimonobambusa genus. This study reported the chloroplast genome of the C. hirtinoda.
Subject(s)
Genome, Chloroplast , Base Composition , Microsatellite Repeats/genetics , Phylogeny , Poaceae/geneticsABSTRACT
Chimonobambusa hejiangensis is a kind of bamboo that has excellent edible and economic value, which is endemic to southwest China. The study used next-generation sequencing to obtain the complete chloroplast (cp) genome sequence of C. hejiangensis. The cp genome of C. hejiangensis has a total length of 138,908 bp, and consisted of an 82,495-bp large single-copy region, an 12,743-bp small single-copy region, and two 21,835-bp IR regions. In total, 112 unique genes were found in the cp genome, including 77 protein coding, 31 tRNA, and 4 rRNA genes. Phylogenetic analysis indicated that C.hejiangensis and C. tumidissinoda are sister species within the Arundinarieae genus, where Chimonocalamus and Ampelocalamus are more closely related to them.
ABSTRACT
BACKGROUND: Isoetes yunguiensis Q. F. Wang & W. C. Taylor is a lycophyte of an ancient genus, and it is endemic to China. It is a first-class protected plant in China. This living fossil is used in paleoecology and studies on the evolution of Lycophytes in the Yunnan-Guizhou Plateau. In recent years, human activities have caused the disappearance of several wild populations, and the number of plants in the existing populations is low. Study of the genetic structure, distribution pattern, and historical dynamics of I. yunguiensis in all areas of its distribution is of guiding significance for its rational and effective protection. METHODS: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to study the genetic diversity and structure of I. yunguiensis, and noncoding chloroplast DNA (cpDNA) sequences were used to study the pedigree, population dynamics history, and glacial shelter of I. yunguiensis. A maximum entropy model was used to predict the past, present, and future distribution patterns of I. yunguiensis. RESULTS: Analysis with EST-SSR markers revealed that I. yunguiensis showed high genetic diversity and that genetic variation was significantly higher within populations than between populations. Based on cpDNA data, it was concluded that there was no significant geographic pedigree in the whole area of I. yunguiensis distribution (NST = 0.344 > GST = 0.183, p > 0.05); 21 haplotypes were detected using DnaSP v5. Neutral test and LAMARC simulation showed that I. yunguiensis has experienced rapid expansion in recent years. The maximum entropy model predicted that the potential distribution area of I. yunguiensis in the last glacial maximum period has increased significantly compared with the present distribution area, but the future distribution area did not show substantial changes.
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In this study, Ophiorrhiza guizhouensis, a new species of Rubiaceae from south-western China, is described and illustrated. The new species is morphologically similar to O. japonica, but differs from the latter by having terete stems which are densely hirtellous, usually persistent ciliate stipules with well-developed colleters inside the base of the stipule, shorter corolla tubes and shorter stamens and styles.
ABSTRACT
In order to reveal the effects of temperature on the growth and development of Aglossa dimidiata parasitized on Litsea coreana, a laboratory experiment was conducted to study the mean development duration, development rate, and survival rate of A. dimidiata at its different growth stages at 31 degrees C, 28 degrees C, 25 degrees C, 22 degrees C, and 19 degrees C, with the development threshold temperature and effective accumulated temperature for different growth stages calculated. Temperature had significant effects on the developmental duration. Except that the development duration of egg was shortened with increasing temperature, the development durations of larva, pupa, and immature A. dimidiata were the shortest at 25 degrees C, being 249.53 +/- 23.83, 12.94 +/- 1.27, and 273.00 +/- 24.19 days, respectively. There existed significant relationships between the development rates of A. dimidiata at its different growth stages and temperature, with positive linear relationship at egg stage, and quadratic relationship at larva, pupa, and immature stages. Temperature also had significant effects on the survival rate of A. dimidiata. The survival rates of A. dimidiata at its different growth stages were all the highest at 25 degrees C, being 94.0%, 73.8%, 91.3%, and 63.4% for the egg, larva, pupa, and immature A. dimidiata, respectively, followed by at 22 degrees C and 19 degrees C, and the lowest at 31 degrees C. No larva and pupa could survive at 31 degrees C, suggesting that A. dimidiata was not resistant to high temperature. The development threshold temperature for egg, larva, pupa, and immature A. dimidiata was 13.21 degrees C, 17.12 degrees C, 14.76 degrees C, and 16.47 degrees C, and the effective accumulated temperature was 117.94, 870.88, 149.70, and 1442.75 day-degree, respectively. The results coincided with the fact that the A. dimidiata reproduced 2 or 3 generations a year in Xifeng area of Guizhou, Southwest China.
