Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra)

Genome-Wide Microsatellites in Acanthopagrus latus: Development, Distribution, Characterization, and Polymorphism

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus.

Genome-Wide Survey and Analysis of Microsatellites in Waterlily, and Potential for Polymorphic Marker Development

Waterlily (Nymphaeaceae), a diploid dicotyledon, is an ornamental aquatic plant. In 2020, the complete draft genome for the blue-petal waterlily (Nymphaea colorata) was made available in GenBank. To date, the genome-wide mining of microsatellites or simple sequence repeats (SSRs) in waterlily is still absent. In the present study, we investigated the characteristics of genome-wide microsatellites for N. colorata and developed polymorphic SSR markers across tropical and hardy waterlilies. A total of 238,816 SSRs were identified in 14 N. colorata chromosomes with an average density of 662.60 SSRs per Mb, and the largest number of SSRs were present on chromosome 1 (n = 30,426, 705.94 SSRs per Mb). The dinucleotide was the most common type, and AT-rich repeats prevail in the N. colorata genome. The SSR occurrence frequencies decreased as the number of motif repeats increased. Among 2442 protein-coding region SSRs, trinucleotides, accounting for 63.84%, were the most abundant. Gene ontology terms for signal transduction (e.g., GO: 0045859 and GO: 0019887) and the lipoic acid metabolism (ko00785,) were overrepresented in GO and KEGG enrichment analysis, respectively. In addition, 107,152 primer pairs were identified, and 13 novel polymorphism SSR markers were employed to distinguish among nine waterlily cultivars, of which Ny-5.2 and Ny-10.1 were the most informative SSR loci. This study contributes the first detailed characterization of SSRs in N. colorata genomes and delivers 13 novel polymorphism markers, which are useful for the molecular breeding strategies, genetic diversity and population structure analysis of waterlily.

Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)

Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage 'TO1000.' Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14-0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers

Akebia trifoliata (Lardizabalaceae) is an important medicinal plant with multiple pharmacological effects. However, the lack of genomic information had limited the further excavation and utilization of this plant. An initial survey of the genome A. trifoliata was performed by next-generation sequencing, and then the genome size was inferred by flow cytometry. The whole genome survey of A. trifoliata generated 61.90 Gb of sequence data with approximately 95.51 × coverage. The genome size, heterozygosity and GC content obtained by k-mer analysis were almost 648.07 Mb, 0.72% and 36.11%, respectively. The genome size calculated by flow cytometry was 685.77 Mb, which was consistent with the results of genome survey. A total of 851,957 simple sequence repeats (SSR) were identified in the A. trifoliata genome. Twenty-eight phenotypic traits and thirty pairs of SSR primers were selected for the analysis of the genetic diversity of 43 accessions of cultivated A. trifoliata. The results showed that 216 bands were generated by 30 pairs of SSR primers, of which 189 (87.5%) were polymorphic. In addition, the phenotypes and SSR markers were used for cluster analysis of 43 cultivated accessions. The results of the two clustering methods were partially consistent. The genome survey of A. trifoliata demonstrated that the genome size of this plant was about 648.07 Mb. In the present study, the size and characteristics of the genome of A. trifoliata were reported for the first time, which greatly enriched the genomic resources of A. trifoliata for the further research and utilization.

Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles

Latest advancement of omics technologies allows in-depth characterization of venom compositions. In the present work we present a proteomic study of two snake venoms of the genus Naja i.e., Naja naja (black cobra) and Naja oxiana (brown cobra) of Pakistani origin. The present study has shown that these snake venoms consist of a highly diversified proteome. Furthermore, the data also revealed variation among closely related species. High throughput mass spectrometric analysis of the venom proteome allowed to identify for the N. naja venom 34 protein families and for the N. oxiana 24 protein families. The comparative evaluation of the two venoms showed that N. naja consists of a more complex venom proteome than N. oxiana venom. Analysis also showed N-terminal acetylation (N-ace) of a few proteins in both venoms. To the best of our knowledge, this is the first study revealing this posttranslational modification in snake venom. N-ace can shed light on the mechanism of regulation of venom proteins inside the venom gland. Furthermore, our data showed the presence of other body proteins, e.g., ankyrin repeats, leucine repeats, zinc finger, cobra serum albumin, transferrin, insulin, deoxyribonuclease-2-alpha, and other regulatory proteins in these venoms. Interestingly, our data identified Ras-GTpase type of proteins, which indicate the presence of extracellular vesicles in the venom. The data can support the production of distinct and specific anti-venoms and also allow a better understanding of the envenomation and mechanism of distribution of toxins. Data are available via ProteomeXchange with identifier PXD018726.

SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences

Microsatellites or simple sequence repeats (SSRs) are short tandem repeats of DNA widespread in genomes and transcriptomes of diverse organisms and are used in various genetic studies. Few software programs that mine SSRs can be further used to mine polymorphic SSRs, and these programs have poor portability, have slow computational speed, are highly dependent on other programs, and have low marker development rates. In this study, we develop an algorithm named Simple Sequence Repeat Molecular Marker Developer (SSRMMD), which uses improved regular expressions to rapidly and exhaustively mine perfect SSR loci from any size of assembled sequence. To mine polymorphic SSRs, SSRMMD uses a novel three-stage method to assess the conservativeness of SSR flanking sequences and then uses the sliding window method to fragment each assembled sequence to assess its uniqueness. Furthermore, molecular biology assays support the polymorphic SSRs identified by SSRMMD. SSRMMD is implemented using the Perl programming language and can be downloaded from https://github.com/GouXiangJian/SSRMMD.