<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>

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

<div>Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. 
 
Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. 
 
Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii. &nbsp;</div>

<div>The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii&nbsp;</div>

<div>Background: Mycobacteroides chelonae M77 isolated in a targeted Mycobacterial isolation study from bovine raw milk was whole genome sequenced (CP041150.1), followed by comparative genomics study for better understanding of the organism with special focus on its virulence and antibiotic resistance pattern. This is probably the first whole genome sequence (WGS) of M.cheloane submitted in NCBI database from India.&nbsp; 
 
Methods: The WGS has been carried out in Illumina Next Seq 500 platform and then assembled resulting in a genome of 5.12 MB. The assembled genome was annotated in RASTtk and viewed by SEED for its detailed analysis. Pathogen Finder 1.1 and Res Finder 3.1 soft wares were applied for knowing the isolate pathogenecity and antibiotic profiling respectively. Mauve analysis was carried out to know the genomic re-arrangements. 
 
Result: Pathogen Finder 1.1 showed that M77 was non-pathogenic and Res Finder 3.1 server reveals it is susceptible to most of the antibiotics. Mauve analysis for alignment of isolate revealed no significant re-arrangement of genomic segment. The whole analysis showed that the genome of M77 is tight genome with not much variation in relation to previous complete genomes reported and is non-pathogenic and sensitive to most of the antibiotics.</div>

<div>Whole Genome Sequencing and Analysis of Mycobacteroides chelonae M77 Isolated from Cow Milk from the Hill State of Meghalaya, India</div>

<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

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)

Background: Bangana dero is a cyprinid fish species that is classified under the subfamily Labeoninae. It occurs in the streams of China, India and Nepal near the foot of the Himalayan range. B. dero&rsquo;s whole mitochondrial genome has been sequenced and annotated. In this work, the tRNAs, protein-coding genes have been characterized and analyzed the phylogenetic relation of this fish with other cyprinid species. 
 
Methods: Nanopore sequencing was utilized to determine the entire mitochondrial genome of B. dero. Utilizing NEBNext Ultra DNA Library Prep Kit, end-repair was performed on the isolated DNA using the. Barcoding adapter ligation (BCA) and cleaned. Sequencing was done. All the long read bases were trimmed based on lowest base quality score, Q&lt;9. Barcode and adapters sequences were also trimmed using a porechop programme and the statistical graph illustrations were generated and genome assembly was done using Canu1.5. 
 
Result: The mitogenome is 16613 bp and contains 13 protein-coding genes, 2 rRNA genes,&nbsp; 22 tRNA genes, as well as a non-coding region. The nucleotide makeup is A=32.5%, T=25.21%, C=26.51% and G=15.77%, G + C = 42.28% and A+T=57.71%. The clover-leaf secondary structure was found in all tRNAs except tRNA-Ser2, which has no dihydrouridine arm. For 12 out of 13 protein-coding genes, the initiation codon was ATG, but COI used GTG. Methionine and tryptophan are unique among amino acids as they are each encoded by a single codon. Origin of light chain replication (OL) could fold into a hairpin secondary structure and carried a sequence 5&#39;-GGCGG-3&#39; in its stem. A long intergenic spacer of 46 bp was observed between tRNA-Leu1 and ND1. In the phylogenetic study, B. dero clustered closely with the Bangana species (AP013327) and Labeo boggut (NC_029450), a grouping supported by a bootstrap value of 100. This is the first study on the entire mitochondrial DNA analysis of B. dero.

&nbsp;

The Complete Mitochondrial Genome of Bangana dero (Cyprinidae: labeoninae) and its Relationship with Other Labeonin Fishes

The polledness intersexual goat (PIS- -) (Capra hircus), deformed individuals, could have malformed reproductive organs and loss of reproductive function. Here, we first determined the complete mitochondrial genome of Chinese native polledness intersexual goat (PIS- -) is 16,640 nt in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region. As in other mammals and intrastrains, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.5%, T: 27.3%, C: 26.1% and G: 13.1%. The complete mitogenome of the Chinese indigenous breed of goat could provide a basic data for further understanding the contribution of mitochondria in the sex-developmental mechanism, tissue and organ cell deformity of polledness intersexual goat via genomic compare.&nbsp;

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

Comparison of the Complete Chloroplast Genomes in the Astragalus

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

Whole Genome Sequencing and Analysis of Mycobacteroides chelonae M77 Isolated from Cow Milk from the Hill State of Meghalaya, India

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

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

The Complete Mitochondrial Genome of Bangana dero (Cyprinidae: labeoninae) and its Relationship with Other Labeonin Fishes

Comparative analysis the variability of a complete mitochondrial genome of polledness intersexual goat (PIS- -) from China