Background: Astragalus is one of the largest angiosperms and has important economic value. The chloroplast genomes (Cp) of most plants in its family have been sequenced and annotated, but there are fewer studies on the characteristics of the chloroplast genomes and codon usage bias of Astragalus. In this study, we sequenced and annotated the complete chloroplast genomes of three Astragalus species, that systematically compared the chloroplast genome and codon usage characteristics of three Astragalus. 
 
Methods: In this study, we used three Astragalus species as materials. Firstly, we sequenced and assembled their chloroplast genomes. Subsequently, we analyzed the codon usage bias of the chloroplast genomes of the three medicinal Astragalus species using software such as CodonW, CUSP and SPSS. 
 
Result: The results illustrated that the length of Astragalus chloroplast genome ranges from 122,815 bp (A. dahuricus) to 123,729 bp (A. melilotoides Pall.). There were 107-110 genes, including 75-76 protein-coding genes (PCGs), four ribosomal RNA genes (rRNAs) and 28-30 transfer RNA genes (tRNAs). In addition, the results illustrated that codons in three Cp genomes from Astragalus had the same 11 Optimal codons and ending with A/U. The codon usage frequency of five model creatures were compared and the results revealed that the codon preferences of Astragalus and five model creatures were pretty significant, the natural selection was the main factor in codon preference. Our research provides some value for the researches of chloroplast genetic engineering and molecular breeding in Astragalus.

Comparison of the Complete Chloroplast Genomes in the Astragalus

Background: Euchresta tubulosa is a medicinal plant in the Fabaceae family, traditionally used in Chinese herbal medicine for treating ailments such as sore throat and esophageal cancer. Despite its pharmacological importance and endangered status, no complete chloroplast genome data had been reported for this species or its genus prior to this study. Chloroplast genomes, being highly conserved and maternally inherited, serve as powerful tools for species identification, phylogenetic inference and genetic diversity assessment in plants. 
 
Methods: Fresh leaves of E. tubulosa were collected and genomic DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method. High-throughput sequencing was carried out on the Illumina NovaSeq6000 platform. Clean reads were assembled into a complete chloroplast genome using NovoPlasty, with a related species as the seed reference. Genome annotation was performed using DOGMA and validated manually. Codon usage patterns were analyzed using RSCU values and simple sequence repeats (SSRs) were identified with MISA software. A maximum likelihood phylogenetic tree was constructed using PhyML, based on complete chloroplast genome sequences from 14 related species. 
 
Result: The assembled chloroplast genome of E. tubulosa measured 153,960 bp and exhibited a typical quadripartite structure, comprising a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (IRs). The overall GC content was 36.3%. A total of 127 genes were identified, including 44 related to photosynthesis, 72 involved in self-replication, 5 with other biological roles and 6 hypothetical or unknown genes. Codon usage analysis revealed 31 codons with RSCU &gt; 1, showing a strong bias toward A/U-ending codons. A total of 109 SSR loci were detected, the majority of which were located in intergenic spacer regions. Phylogenetic analysis clearly positioned E. tubulosa as an independent lineage within the Fabaceae, supported by high bootstrap values. The genomic information provided by this study lays a foundation for future research in molecular taxonomy, phylogenetics and conservation of this endangered medicinal plant.

Features and Phylogenetic Analysis of the Chloroplast Genome of the Medicinal Plant Euchresta tubulosa

Background:&nbsp;Entada phaseoloides&nbsp;(L.) Merr (Fabaceae)&nbsp;is a large woody climber that is found widely in southern China and other tropical and subtropical areas worldwide. The genus Entada&nbsp;contains ~30 species, and E. phaseoloides&nbsp;is most commonly found in China. The E. phaneroneura&nbsp;and E. pervillei&nbsp;are endangered species. Previous studies had focused on medicinal components, transcriptional regulation, and nuclear genomes. The chloroplast genome of Entada&nbsp;has not been reported, and little is known about the phylogenetic relationships within the Entada. In this study, we performed short-read sequencing of E. phaseoloides&nbsp;and assembled and analyzed its chloroplast genome.

Methods:&nbsp;Dry specimen leaves of E. phaseoloides&nbsp;were subjected to DNA extraction and sequenced using the Illumina Novoseq platform. The chloroplast genome was assembled using Get Organelle, annotated using CPGAVAS2 and Geneious Prime. Repeat sequences and SSR analysis were performed using the Reputer and MISA programs, respectively.&nbsp;Phylogenetic analyses were performed using IQTREE and MrBayes software.

Result:&nbsp;The complete chloroplast genome of E. phaseoloides&nbsp;is 159,963 bp in length and has a quadripartite structure with large single copy of 89,972 bp and a small single copy of 19,309 bp separated by inverted repeats of 25,341 bp. A total of 112 genes in E. phaseoloides&nbsp;comprised 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. The distribution of simple sequence repeats and long repeat sequences was determined. We carried out phylogenetic analysis based on homologous protein-coding genes among 21 species derived from Fabaceae. We found that the phylogeny was largely congruent with prior hypotheses about the position of E. phaseoloides&nbsp;in evolutionary branches. The E. phaseoloides&nbsp;has a closer relationship with the Piptadeniastrum africanum.

Complete Chloroplast Genome and Comparative Analysis of Entada phaseoloides (Fabaceae)

<div>Background: &ldquo;Lasona&rdquo; (Allium cepa var. aggregatum G. Don) is a multi-bulb cultivar commonly grown in the Northern Philippines as an annual crop. This, together with bulb onion, are the two main types of onions produced in the country, but the majority of onions exported from the Philippines are the latter. However, despite its importance to the human diet, no complete chloroplast genome sequence has been reported to date. Hence, the assembled plastome can be utilized as a resource for distinguishing the taxon and elucidating its evolutionary relationship with other Allium species, particularly within the aggregatum group. 
 
Methods: Using Illumina sequencing data, we assembled and annotated the complete chloroplast genome of A. cepa var. aggregatum accession from the germplasm collection of the Institute of Crop Science, University of the Philippines, Los Ba&ntilde;os, Laguna. Moreover, the morphology of the genotyped accession was characterized to ensure that the genome assembled is attributed to the correct taxon. The voucher specimen (ICROPS 1374) was deposited at the Philippine Herbarium of Cultivated Plants of the Institute of Crop Science. 
 
Result: The complete chloroplast (cp) genome had a sequence length of 153,587-bp long, with 36.8% overall GC content. A total of 126 functional genes were found, comprising 80 mRNA genes, 38 tRNA genes and 8 rRNA genes. We annotated 43 genes that code for photosynthesis, 29 genes for self-replication and 6 other genes for other functions. This is the first complete chloroplast genome of Allium cepa var. aggregatum. The phylogenetic analysis of the assembled genome, together with 21 other Allium accessions and 12 other Amaryllidaceae species, revealed that the A. cepa accessions formed a distinct clade despite infraspecific plastome variations. Comparison among earlier published plastomes of A. cepa showed that the assembled A. cepa var. aggregatum chloroplast genome was distinct in sequence length and composition. The observed differences could be utilized to further elucidate differences needed for varietal identification. 
&nbsp;</div>

The Complete Chloroplast Genome of &ldquo;Lasona&rdquo; (Allium cepa var. Aggregatum G. Don), an Important Indigenous Vegetable in the Northern Philippines

<div>Background: Comparative study of the complete chloroplast genomes of some species in the Subtribe Asclepiadeae was conducted to evaluate the variations and similarities between the species and to resolve the phylogenetic relationship within the subtribe. P. tomentosa has been used for medicinal uses in Saudi Arabia, Middle East, Africa and Brazil. It is used often in cosmetics and tanning industries, although it&rsquo;s very well utilized as a traditional medicine in many civilizations. 
 
Methods: The genomes were compared using Mvista Bioinformatics tools to evaluate the inverted repeats (IR), large single copy (LSC) and small single copy (SSC) regions and also the border junctions were visualized with IR scope to express the expansion and contraction of the circular genome structure. While SSR markers were determined using the Reputer program, the genome map was done using OGDRAW (OrganellarGenomeDRAW). 
 
Result: Observed variations of the Mvista alignments is mainly at the coding regions of the sequences, while IR borders were varied at the SSC region of A. nivea genome; with ycf1 and rps19 due to evolutionary events. The genome sizes of C. procera are 166,010 bp, P. tomentosa 164,213bp, A. nivea 161,592 bp and C. wilfordii 161,180 bp. GC contents of A. nivea, C. wilfordii and P. tomentosa are 38% respectively; while C. procera is the least with 37%.; total SSR markers as well as the circular genome map were presented in this study.</div>

<div>Comparative Chloroplast Genome Analysis and Evolutionary Relationships in Some Species of Asclepiadeae, Apocynaceae</div>

Background: Codon usage bias is a widespread phenomenon in many organisms, including higher plants and plays an important role in regulating gene expression efficiency and accuracy. As an important forage species with high nutritional value, Medicago sativa (alfalfa) has been extensively utilized not only in traditional breeding but also in molecular genetic improvement. Understanding the characteristics of codon preference in its organelle genomes can provide valuable guidance for optimizing gene design and enhancing the expression of exogenous genes in alfalfa or related species. 
 
Methods: A total of 30 mitochondrial and 51 chloroplast high-quality coding sequences were obtained from the NCBI database. Codon usage patterns and preferences were analyzed using CodonW, R, MEGA and Excel. 
 
Result: The effective number of codons (ENC) in mitochondria ranged from 44.73 to 61.0, with an average GC content of 0.42 and GC content at the third codon position (GC3s) of 0.37. In chloroplasts, the ENC ranged from 38.90 to 57.76, with an average GC content of 0.37 and GC3s of 0.27. Analyses using ENC-plot, neutrality plot and PR2 bias analysis suggested that codon usage bias in Medicago sativa is influenced by both natural selection and mutation pressure. Twelve optimal codons were identified in mitochondria (mostly ending in &lsquo;A&rsquo; and &lsquo;U&rsquo;) and fourteen in chloroplasts, also showing a preference for &lsquo;A/U&rsquo;-ending codons. 
&nbsp;

Comparative Analysis of Mitochondrial and Chloroplast Genomes in Alfalfa (Medicago sativa L.)

<div>Background:&nbsp;The DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species.&nbsp; 
 
Methods:&nbsp;DNA barcoding of 9 chloroplast genes (rbcL, matK, trnH-psbA, accD-psaI, ndhA, psbE-petL, Rpl32-trnL, trnW-psaJ, trnSGCU-trnGGCC) were used to provide the theoretical basis for species identification, genetic diversity analysis of lotus population collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequence products were analyzed using the MEGA X program. 
 
Result:&nbsp;The results showed that high levels of haplotype diversity (Hd), ranging from 0.618-0.869 and low levels of nucleotide diversity (Pi), ranging from 0.180 &times; 10-3-3.280 &times; 10-3 base on a total of nine gene regions of chloroplast genome. The neutrality tests show an excess of rare nucleotide position variations in individuals&rsquo; white lotus and derived haplotypes recent expansion. While the evolution of the individuals in the pink lotus may have to decrease. The phylogenetic analyses indicated that combined sequences were not insufficient to make a difference to the DNA barcoding in the individual&rsquo;s lotus of the N. nucifera species this is in the study. The standardized and accurate barcode information of lotus is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Nelumbonaceae germplasm resources.</div>

Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode

<div>Mungbean is an important pulse crop and it is mainly cultivated in Asia for human consumption. Its small genome and diploid nature make it a well-suited model organism among legume crops. Thus, cost-effective, reliable and highly polymorphic molecular markers distributing the whole genome are needed for diversity, mapping and functional genomics studies in this model species. The whole-genome sequence of mungbean was obtained and used as a source of identification of simple sequence repeats (SSR). The sequence reads were aligned and SSRs detection was performed using the Phobos plugin tandem repeat finder in the Geneious software program. A total of 12 mungbean genotypes were selected to validate the newly developed SSR markers.&nbsp;In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats were identified from the mungbean genome. The tri-repeats were the most abundant (26.10%), followed by hexa (20.82%), penta (20.45%), tetra (17.65%) and di-repeats (14.95%). We designed 1330 SSR primers based on the genomic sequence of flanking perfect SSRs (Di and tri-repeats). Among them, 50 SSR primers uniformly distributed across the 11 mungbean chromosomes were selected and used to validate 12 mungbean genotypes. The newly developed genomic SSR markers generated in the present study are a valuable genomic resource for the mungbean breeding programs.</div>

Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

<div>Background: Jordanian Awassi sheep (Ovis aries) is the dominant fat tail sheep breed that appeals to customers because of its various production systems, including fiber, meat and milk. This report is the first whole ewe genome sequence (WGS) of O. aries submitted in the NCBI database from Jordan. 
 
Methods: 64 Paired-end sequencing libraries were constructed and subjected to Illumina Hiseq 2500 sequencing system. High-quality reads were aligned against the reference sheep genome and detecting comprehensive sources (SNPs, InDels, SV, CNVs) of genetic variations. We have deposited data sequences at the NCBI under SRA (sequence reads archives) under the accession numbers SRR11128863, PRJNA574879. 
 
Result: Genome resequencing of Jordanian Awassi ewe was carried out with approximately 93.88 Gb with a mapping rate and effective mapping depths were 99.28% and 36.32. Around 19 million SNPs, 3,6 million InDels, 35,180 Structure variation and 13,524 copy number variation among the Jordanian ewe genome were detected. This wide range of genetic variation provides a framework for further genetic studies that will help understand the molecular basis underlying phenotypic variation of economically important traits in sheep and improve intrinsic defects in domestic sheep breeds.</div>

​Re-sequencing of Whole Genome Jordanian Awassi Ewes using Hiseq Sequencing Technology: Major Step Towards Sheep Genomic Selection

<div>Background: Dates palm is one of the most economically important plant mainly cultivated in Northern Africa, Middle East and South Asia. India is the largest importer of date fruit. In India, Dates palm are cultivated majorly in Gujarat and Rajasthan. Dates farmers facing several problem in India due to lack of scientific resources. Plant growth promoting rhizobacteria (PGPR) are naturally associated with plants and it improves plant growth and yield by providing growth supplements, increasing tolerance to stressful conditions and providing resistance to fungal/bacterial diseases. We have isolated a PGPR belonging to Exiguobacterium species TNDT2 from Indian dates palm Phoenix dactylifera, in Dindigul region, Tamilnadu, India. The organism&rsquo;s genome was sequenced and identified several potential plant growth promoting (PGP) genes.&nbsp; 
 
Methods: The organisms genome was sequenced using Whole genome shotgun sequencing method in Illumina platform. Sequences are analysed using various bioinformatics tools and assembled using Velvet assembler. Contigs are annotated using RAST server and deposited in NCBI.&nbsp; 
 
Result: The isolated strain revealed various genetic determinants required for plant growth promotion. This study presents the first report of Exiguobacterium TNDT2 genome from Dates tree rhizosphere. Whole genome analysis and genome annotation reveals that, its genome consist of a 2,891,840 bp chromosome encoding over 3062 proteins, with a 51.63% GC content. Strain TNDT2 encodes a wide repertoire of proteins for plant growth promotion, heavy metal detoxification (cadmium, arsenic, mercury, copper and tellurite), Multi-drug resistance and stress resistance (Heat, cold and salt). Based on this study, Exiguobacterium sp. TNDT2 can be recognized as an important organism with a potential to be incorporated into agricultural practice of&nbsp;Date palm.</div>

<div>Whole Genome Sequencing and Genome Annotation of PGPR &lsquo;Exiguobacterium sp. TNDT2&rsquo; Isolated from Dates Palm Tree Rhizospheric Soil</div>

Comparison of the Complete Chloroplast Genomes in the Astragalus

Features and Phylogenetic Analysis of the Chloroplast Genome of the Medicinal Plant Euchresta tubulosa

Complete Chloroplast Genome and Comparative Analysis of Entada phaseoloides (Fabaceae)

The Complete Chloroplast Genome of “Lasona” (Allium cepa var. Aggregatum G. Don), an Important Indigenous Vegetable in the Northern Philippines

Comparative Chloroplast Genome Analysis and Evolutionary Relationships in Some Species of Asclepiadeae, Apocynaceae

Comparative Analysis of Mitochondrial and Chloroplast Genomes in Alfalfa (Medicago sativa L.)

Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode

Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

Re-sequencing of Whole Genome Jordanian Awassi Ewes using Hiseq Sequencing Technology: Major Step Towards Sheep Genomic Selection

Whole Genome Sequencing and Genome Annotation of PGPR ‘Exiguobacterium sp. TNDT2’ Isolated from Dates Palm Tree Rhizospheric Soil