A near-complete genome assembly of Thalia dealbata Fraser (Marantaceae).

This study presents a chromosome-level, near-complete genome assembly of Thalia dealbata (Marantaceae), a typical emergent wetland plant with high ornamental and environmental value. Based on 36.99 Gb PacBio HiFi reads and 39.44 Gb Hi-C reads, we obtained a 255.05 Mb assembly, of which 251.92 Mb (98.77%) were anchored into eight pseudo-chromosomes. Five pseudo-chromosomes were completely assembled, and the other three had one to two gaps. The final assembly had a high contig N50 value (29.80 Mb) and benchmarking universal single-copy orthologs (BUSCO) recovery score (97.52%). The T. dealbata genome had 100.35 Mb repeat sequences, 24,780 protein-coding genes, and 13,679 non-coding RNAs. Phylogenetic analysis revealed that T. dealbata was closest to Zingiber officinale, whose divergence time was approximately 55.41 million years ago. In addition, 48 and 52 significantly expanded and contracted gene families were identified within the T. dealbata genome. Moreover, 309 gene families were specific to T. dealbata, and 1,017 genes were positively selected. The T. dealbata genome reported in this study provides a valuable genomic resource for further research on wetland plant adaptation and the genome evolution dynamics. This genome is also beneficial for the comparative genomics of Zingiberales species and flowering plants.

Microsatellite markers for the Chinese endangered and endemic orchid Cymbidium tortisepalum (Orchidaceae).

PREMISE OF THE STUDY: Microsatellite primers were developed in the Chinese endangered and endemic orchid, Cymbidium tortisepalum, to investigate its genetic diversity and population genetic structure, and to identify its varieties. METHODS AND RESULTS: Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol, 15 primer sets were identified in two wild populations. The number of alleles per locus ranged from two to six, with a mean of 3.5. The observed and expected heterozygosities varied from 0.250 to 0.917 and from 0.228 to 0.841, respectively. All of these primers successfully amplified in the congener C. goeringii, and 12 were found useful in C. faberi and C. sinense. CONCLUSIONS: These markers will facilitate further studies on the population genetics and molecular identification of C. tortisepalum, its varieties, and other congener species.

Complete chloroplast genome sequence of the drought and heat-resistant Chinese alfalfa landrace, Medicago sativa 'Deqin'.

Medicago sativa 'Deqin' is an excellent alfalfa landrace with strong drought and heat resistant which can grow and propagate very well in Deqin, a xerothermic valley of Jinsha River, China. In this study, the complete chloroplast genome of M. sativa 'Deqin' was assembled. The complete chloroplast genome of M. sativa 'Deqin' represents a typical circular with 125,470 bp in length, containing one inverted repeat (IR) region. Gene prediction revealed 110 genes encoding 76 proteins, 30 transfer RNAs, and four ribosome RNAs. Three genes (rps16, rpl22 and infA) are absent. The overall GC content is 33.9%. The phylogenetic analysis revealed that M. sativa 'Deqin' belonged to the IR lacking clade, and was closely related to M. sativa with a 100% bootstrap support.

Response and intraspecific differences in nitrogen metabolism of alfalfa (Medicago sativa L.) under cadmium stress.

Pot experiments were carried out to evaluate the response and intraspecific differences in nitrogen metabolism of 20 alfalfa cultivars under cadmium stress. To the aim, exogenous cadmium was added into soil with concentration of 0 (control) and 50 mg kg-1. Results showed that 20 alfalfa were ranked as following according to response index: Guochan (550.93) > Deqin (372.50) > Caoyuan No.1 (350.26) > Queen (345.45) > Xinmu No.2 (344.43) > Longzhong (274.85) > Victoria (233.13) > Emperor (233.13) > Giant (192.29) > Qianjing (101.21) > Xinjiangdaye (75.72) > Algonuin (-32.55) > Duoye (-62.44) > Altay (-102.77) > Sandeli (-155.02) > Turist (-193.24) > Gannong No.1 (-199.22) > Sijiwang (-245.14) > Zhongmu No.1 (-245.48) > WL525HQ (-268.26). Guochan was identified as cadmium tolerant cultivar. Compared with the control group, its plant height increased by 40.96%, shoot and root biomass respectively increased by 18.10% and 70.19%, total nitrogen content in shoot and root respectively increased by 26.69% and decreased by 12.59%, nitrate content decreased by 7.05%, content of ammonium, proline, free amino acid and soluble protein respectively increased by 13.67%, 89.63%, 28.09% and 14.86%, activity of nitrate reductase, glutamine synthetase, glutamate synthase and glutamate dehydrogenase increased respectively 58.52%, 36.63%, 97.79% and 75.44%. WL525HQ, its above indicators appeared significant differences with those of Guochan, was identified as cadmium sensitive cultivar. In conclusion that the nitrogen metabolism process played an important role for alfalfa to adapt cadmium stress, and the response of nitrogen metabolism to cadmium stress varied with different alfalfa cultivars.

[Computational analysis of signal peptide-dependent secreted protein in Caenorthaditis elegans ws123].

The internet-based softwares SignalP v3.0, TargetP v1.01, big-PI predictor and TMHMM v2.0 were combined to predict the signal peptides and the signal peptide-dependent secreted proteins from the 19,855 ORFs in Caenorthaditis elegans ws123 genome. 1,990 proteins were predicted to be secreted and to contain signal peptides among 19,855 proteins, among which 1,936 have SignalPase I signal peptide (containing 41 with RR-motif signal peptide), 53 have SignalPase II signal peptide and one has SignalPase IV signal peptide. The signal peptides of 742 secreted proteins include only H-domain and C-domain, but no typical N-domain; the signal peptides of other 1,248 secreted proteins include all three domains. Although the amino acids constitution of the SignalPase I signal peptides were similar in general between Caenorthaditis elegans and prokaryote, there were apparently small differences, and the amino acid composition of Caenorthaditis elegans are more diverse and less conserved. But there are distinct differences on the amino acid composition of SignalPase II signal peptides. The signal peptides of Caenorthaditis elegans were more diverse than unicellular eukaryotic organism. The signal peptides of a few proteins were exactly the same. We used the BLAST 2 SEQUENECES aligning method to compare the homology among the secreted proteins with the same signal peptides. The alignment results indicated that the genes sharing the same signal peptide sequences were homologous to each other and were likely to have arisen from gene duplication.

[Genetic diversity analysis of alfalfa floral properties.].

Genetic mutations of alfalfa floral properties,including calyx diameter, coronary length, flower number per raceme, raceme number per twig, flower number per unit area, percentage of flicked flowers, excreted nectar volume, sugar concentration in nectar and contents of sucrose, fructose and glucose in nectar,have been studied with both morphological markers and RAPD markers. The results showed that the genetic variation of floral properties is from 0.80% to 92.30%, of which the content of glucose was the most significant one with the variation from 0.01 to 0.53 mumol/L (p0.05), and the sugar concentration was the most insignificant one (P>0.05). RAPD analysis showed that variances of genetic distances was from 0.21 to 0.35, among which the most significant one was WL323 and Shanbei, and the most insignificant one was Derby and Prime. Thus it can be seen that genetic diversity of floral properties among these varieties of alfalfas is abundant.