Dinucleotide Repeat Motifs Research Articles

Effect of the switch status of Helicobacter pylori outer inflammatory protein A on gastric diseases

Helicobacter pylori OipA (Outer Inflammatory Protein A) is an outer membrane protein that takes role in the adherence and colonization to the stomach. oipA gene expression is regulated by the slipped-strand mispairing mechanism through a hypermutable CT dinucleotide repeat motif in the 5΄ region. Alterations in the CT number repeats cause frame-shift mutations to result in phase variation of oipA expression. While a functional “On” status has been recognized as a risk factor for peptic ulcer diseases and gastric cancer in many studies, some controversial findings still exist. To this end, this study compiled the sequence data of oipA from 10 different studies between 2000–2019 and 50 oipA DNA sequences from our own research that examined the relationship between the phase On/Off status of oipA and gastric diseases based on CT repeat number. Overall, we have reached 536 oipA DNA sequences from patients. This large collection of oipA sequences first clarified the absolute conservation of the peptide-pentamer of FWLHA for phase ‘’On’’ status, suggesting this pentamer as a superior marker for the determination of oipA status than counting the number of CT repeats. Combining the sequence and patient data, we have re-analyzed the association between the ‘‘On’’ status of oipA and gastric diseases. Our results showed a strong association between oipA ‘‘On’’ status and gastric cancer supporting previous findings. We also investigated the AlphaFold2 computed structure of OipA that adopts a beta-barrel fold closely resembling to the autotransporter family of H. pylori. Altogether, this study confirms a strong association between oipA ‘‘On’’ statuses and severe gastrointestinal diseases like cancer and provides useful insights into the FWLHA pentamer as an indicator of “On” status of oipA putative autotransporter function rather than CT repeats number.

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB.

The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12-<20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, "Cashew Microsatellite Database (CMDB)," was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species.

Genomic microsatellite characteristics analysis of Dysommaanguillare (Anguilliformes, Dysommidae), based on high-throughput sequencing technology.

Microsatellite loci were screened from the genomic data of Dysommaanguillare and their composition and distribution were analysed by bioinformatics for the first time. The results showed that 4,060,742 scaffolds with a total length of 1,562 Mb were obtained by high-throughput sequencing and 1,160,104 microsatellite loci were obtained by MISA screening, which were distributed on 770,294 scaffolds. The occurrence frequency and relative abundance were 28.57% and 743/Mb, respectively. Amongst the six complete microsatellite types, dinucleotide repeats accounted for the largest proportion (592,234, 51.05%), the highest occurrence frequency (14.58%) and the largest relative abundance (379.27/Mb). A total of 1488 microsatellite repeats were detected in the genome of D.anguillare, amongst which the hexanucleotide repeat motifs were the most abundant (608), followed by pentanucleotide repeat motifs (574), tetranucleotide repeat motifs (232), trinucleotide repeat motifs (59), dinucleotide repeat motifs (11) and mononucleotide repeat motifs (4). The abundance of microsatellites of the same repeat type decreased with the increase of copy numbers. Amongst the six types of nucleotide repeats, the preponderance of repeated motifs are A (191,390, 43.77%), CA (150,240, 25.37%), AAT (13,168, 14.05%), CACG (2,649, 8.14%), TAATG (119, 19.16%) and CCCTAA (190, 19.16%, 7.65%), respectively. The data of the number, distribution and abundance of different types of microsatellites in the genome of D.anguillare were obtained in this study, which would lay a foundation for the development of high-quality microsatellite markers of D.anguillare in the future.

Development and Characterization of SSR Markers via de Novo Transcriptome Assembly in Apocynum. hendersonii

ABSTRACT To provide a theoretical and practical foundation for the genetic analysis of Apocynum species, SSRs were identified based on the transcriptomic data of A.hendersonii leaves. A total of 50,957 unigenes containing 5 660 SSR motifs with an average of 1 SSR locus per 9.09 Kb were identified. The dinucleotide repeat motifs were the most prevalent, having 48.23% of the total repeat, with the dominant repeats being AG/CT (1,703) followed by A/T (1,222). Furthermore, the results of genetic relationship analsyis based on the allele polymorphism of the selected SSR primer showed that A. hendersonii and A.venetum grouped into various clades, and those from different regions clusted into different subgroups.These identified SSR markers may provide a foundation for genetic identification, diversity analysis and marker-assisted genetic breeding in Apocynum species.

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

Abstract. Hatta ANNL, Sukma D, Maskromo I, Sudarsono. 2022. Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis. Biodiversitas 23: 5122-5131. The coconut (Cocos nucifera L.) genome sequences were available at the chromosome level in 2019, and they can be used to develop the whole genome SSR markers. This study aimed to conduct in silico analysis of the whole coconut genome to mine SSR sequences, design SSR markers distributed across coconut chromosomes, validate the designed primers to generate SSR markers, and use them for the phylogenetic analysis of coconuts. The SSR loci were mined from publicly available coconut genomes. Targeted primers for amplifying 20 dinucleotide SSR loci were selected and used for phylogenetic analysis of coconuts. The SSR mining identified 543,774 dinucleotide repeat motifs across the coconut genome, and most of the dinucleotide SSRs are AG (46.18%) and AT (40.03%) repeats. Primer pairs targeted to amplify 876 SSR loci and distributed in 16 coconut chromosomes were successfully designed and deposited in a public data repository for public access. The 237 SSR primer loci were novel and could generate new SSR markers. Among 20 selected and tested primers, 18 produced SSR markers, and 15 pairs yielded polymorphic markers when used to evaluate 25 coconut accessions. The analysis showed that the designed SSR primers were informative for evaluating coconut genetic diversity and phylogenetic analysis.

Genome-wide survey and genetic characteristics of Ophichthus evermanni based on Illumina sequencing platform.

Ophichthidae fishes limit to continental shelf of all tropical and subtropical oceans and contain more than 350 species, representing the greatest specialization diversity in the order Anguiliformes. In the present study, we conducted a genome survey sequencing (GSS) analysis of Ophichthus evermanni by Illumina sequencing platform to briefly reveal its genomic characteristics and phylogenetic relationship. The first de novo assembled 1.97 Gb draft genome of O. evermanni was predicted based on K-mer analysis without obvious nucleotide bias. The heterozygosity ratio was 0.70%, and the sequence repeat ratio was calculated to be 43.30%. A total of 9016 putative coding genes were successfully predicted, in which 3587 unigenes were identified by gene ontology (GO) analysis and 4375 unigenes were classified into cluster of orthologous groups for enkaryotic complete genomes (KOG) functional categories. About 2,812,813 microsatellite motifs including mono-, di-, tri-, tetra-, penta- and hexanucleotide motifs were identified, with an occurrence frequency of 23.32%. The most abundant type was dinucleotide repeat motifs, accounting for 49.19% of the total repeat types. The mitochondrial genome, as a byproduct of GSS, was assembled to investigate the evolutionary relationships between O. evermanni and its relatives. Bayesian inference (BI) phylogenetic tree inferring from concatenated 12 protein-coding genes (PCGs) showed complicated relationships among Ophichthidae species, indicating a polyphyletic origin of the family. The results would achieve more thorough genetic information of snake eels and provide a theoretical basis and reference for further genome-wide analysis of O. evermanni.

Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

Platostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

Genome-wide development and utilization of Simple Sequence Repeats in Chinese cabbage (&lt;i&gt;Brassica rapa&lt;/i&gt; L. ssp. &lt;i&gt;pekinensis&lt;/i&gt;)

With the complementation of whole-genome sequencing of Chinese cabbage, it is necessary to develop genome-wide Simple Sequence Repeat (SSR) markers and analyse their characteristics, which will bring a revolution in the molecular marker-assisted breeding of Chinese cabbage. In this study distribution and characteristics of SSR loci in the genome of Chinese cabbage 'Chiifu' was analyzed. Finally, a total of 173,892 SSR markers that occurred in 10 chromosomes were identified, and Perfect Repeat Motifs (P type) which is a main form of SSR loci with a mean distance of 1.89 kb/SSR was identified. Among them, mono-, di-, and tri-nucleotide repeat motifs were equally distributed across chromosomes compared with tetra-, penta-, and hexa-nucleotide repeat motifs. The largest proportion of SSR loci consisted of mono- and dinucleotide repeat motifs, which accounted for 93.04% of the total SSR loci. A/T and AT/TA were the most abundant motifs, accounting for 97.61% and 64.05% of the mono- and dinucleotide repeats, respectively. Furthermore, 200 SSR markers were used for the amplification of 12 Chinese cabbage germplasm, in which 30 were highly polymorphic. These SSR markers were further used for the association analyses of flowering time of 190 Chinese cabbage accessions. The results revealed that 9 and 10 alleles were associated with bolting and flowering time, respectivley. The results show that development of SSR markers is feasible and useful in marker assisted selection of Chinese cabbage.

De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing.

Labeo rohita, one of the Indian major carps, is the most popular culture species in Indian subcontinent due to its consumer preference and delicacy. A selective breeding program for harvest body weight has resulted in an average genetic gain of 17% per generation. Transcriptome resource for this species is scanty. Here, we have characterized the liver and muscle transcriptomes of rohu using Roche 454 GS-FLX next generation sequencing platform. In total, 1.2 million reads were generated, de novo assembly and clustering resulted in 4171 transcripts. Out of these, 4171 had significant blast hit against NCBI nr database, and 2130 transcripts were successfully annotated. In total, 289 SSRs were identified with an identification rate of 5.8%, and dinucleotide repeat motifs were observed to be the most abundant SSRs. Further, 2231 putative SNPs were identified with high confidence. Validation of eight putative SNPs using Sanger sequencing resulted in 100% true SNPs. Significant allelic imbalance of M1, M4 and M5 loci between growth selected and control individual were observed. Furthermore, 13 transcription factors were identified in the present study belonging to six different transcription factor families. The present study demonstrated the utility of RNAseq to develop genomics resources in non-model fish species, and the marker resources developed would support the genetic improvement program of this species.

Genome-wide SSR marker development and application in genetic diversity analysis of the red swamp crayfish, Procambarus clarkii (Girard, 1852) in China

Abstract The red swamp crayfish, Procambarus clarkii (Girard, 1852), is currently an economically important aquaculture animal. Its genetic basis has been scarcely reported, however, partly due to the absence of abundant molecular markers in the genome. In this study, Simple Sequence Repeat (SSR) loci were mined, based on genome survey sequencing via the next generation sequence of the red swamp crayfish. A total of 4897 SSR loci were identified, with the most abundant type being the di-nucleotide repeat motifs (75.2%), followed by tri- (20.4%), tetra- (3.8%), penta- (0.5%), and hexanucleotide (0.2%) repeats. In total, 1546 SSR markers were validated to be amplified, and 721 of these were identified as polymorphic SSR markers. Fifty polymorphic SSR markers were randomly selected for the identification of the genetic diversity of the 14 red swamp crayfish populations in China. The expected and observed heterozygosity and polymorphism information content were 0.39, 0.30, and 0.29, respectively, on average. The results indicated a medium genetic diversity among the 14 investigated populations. These probably cluster into three genetic populations. The current study provides abundant genetic markers and information on the 14 populations, which can be helpful for genetic diversity estimation and molecular breeding of the red swamp crayfish.

Development of EST-SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.).

Genetic improvement in coconut relies on exploiting the vast existing diversity among coconut accessions. Robust molecular markers are a pre-requisite for efficient characterization of genetic diversity. Microsatellites or simple sequence repeats (SSRs), mined from expressed sequence tags (ESTs), constitute an important resource for analysis of genetic diversity as they are abundant, polymorphic and represent function regions of the genome. We have identified a total of 318,528 putative EST-SSRs from 130,942 unigenes utilizing a leaf transcriptome dataset of coconut. Among the EST-SSRs, dinucleotide repeats were abundant (219,912; 69.04%) followed by trinucleotide (70,722; 22.2%) and tetra-nucleotide repeats (6281; 1.9%). Among the dinucleotide repeat motifs, the dominant repeat was AG/CT (35.87%), followed by AT/AT (18.59%), while the dominant trinucleotide repeat was AAG/CTT (4.59%). One hundred and twenty EST-SSR primer pairs were designed and utilized to amplify six DNA samples of coconut accessions. Fifty primers (41.7%) produced reproducible polymorphic fragments of expected sizes, from which a total of 10 primers were selected for the diversity assessment in 186 palms of 50 coconut accessions, comprising of 25 each of tall and dwarf accessions. A total of 137 alleles were detected with an average of 13.7 alleles per SSR locus. The number of alleles observed at each locus in the data set ranged from 7 to 22. All the loci showed 100% polymorphism with respect to the samples screened. The average observed heterozygosity was 0.46. The PIC values ranged from 0.79 (CnKGDEST129 and CnKGDEST100) to 0.91 (CnKGDEST117 andCnKGDEST122) with a mean value of 0.85, indicating the capacity of the EST-SSR markers to detect high levels of polymorphism. The cluster analysis revealed that accessions were generally clustered based on their relative similarity and irrespective of their geographic origins. The present study demonstrates the usefulness of transcriptome sequencing as a rapid and cost-effective methodology for the development of molecular markers. The EST-SSR markers generated through this study constitute useful and reliable tools for assessment of genetic diversity and marker-assisted selection in coconut.

Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

Genome survey sequencing of Atractylodes lancea and identification of its SSR markers.

Atractylodes lancea (Thunb.) DC. is a traditional Chinese medicine rich in sesquiterpenes that has been widely used in China and Japan for the treatment of viral infections. Despite its important pharmacological value, genomic information regarding A. lancea is currently unavailable. In the present study, the whole genome sequence of A. lancea was obtained using an Illumina sequencing platform. The results revealed an estimated genome size for A. lancea of 4,159.24 Mb, with 2.28% heterozygosity, and a repeat rate of 89.2%, all of which indicate a highly heterozygous genome. Based on the genomic data of A. lancea, 27,582 simple sequence repeat (SSR) markers were identified. The differences in representation among nucleotide repeat types were large, e.g., the mononucleotide repeat type was the most abundant (54.74%) while the pentanucleotide repeats were the least abundant (0.10%), and sequence motifs GA/TC (31.17%) and TTC/GAA (7.23%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. A total of 93,434 genes matched known genes in common databases including 48,493 genes in the Gene Ontology (GO) database and 34,929 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This is the first report to sequence and characterize the whole genome of A. lancea and will provide a theoretical basis and reference for further genome-wide deep sequencing and SSR molecular marker development of A. lancea.

Skin transcriptome, tissue distribution of mucin genes and discovery of simple sequence repeats in crucian carp (Carassius auratus).

Crucian carp (Carassius auratus) is one of the major freshwater species and important food fish in China. Fish skin acts as the first line of defence against pathogens, yet its molecular and immune mechanism remains unclear. In this study, a de novo transcriptome assembly of C. auratus skin was performed with the Illumina Hiseq 2000 platform. A total of 49,154,776 clean reads were assembled, among which 60,824 (46.86%), 37,103 (28.59%), 43,269 (33.33%) unigenes were annotated against National Center for Biotechnology Information, Gene Onotology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. KEGG Orthology categories were significantly involved in immune system (20.50%), signal transduction (18.04%) and mucosal mucin genes (e.g., muc2, muc5AC, muc5B, muc17, muc18). The high expression of muc18 gene was observed in brain; that of muc2 in intestine; and that of muc5AC in skin, liver, spleen, intestine and muscle. Moreover, the potential 28,928 simple sequence repeats with the three most abundant dinucleotide repeat motifs (AC/GT, AG/CT, AT/AT) were detected in C. auratus. To authors' knowledge, this is the first report to describe the transcriptome analysis of C. auratus skin, and the outcome of this study contributed to the understanding of mucosal immune response of the skin and molecular markers in cyprinid species.

Genome Survey Sequence and the Development of Simple Sequence Repeat (SSR) Markers in Erianthus arundinaceus

Erianthus arundinaceus possesses high biomass, vigor, ratoonability and resistance to biotic and abiotic stresses and is considered to be an ideal species for improving sugarcane. In this study, a genome survey sequence was performed in E. arundinaceus, and SSR markers were developed based on a genome survey sequence. A total of 167.36 Gb raw data were obtained and were assembled into 3161 Mb genome sequences, including 15,238,738 scaffolds. The genome size was estimated to be approximately 3.23 Gp based on kmer analysis. In total, 36,616 SSR motifs were identified and characterized, including 60.69% dinucleotide, 34.27% trinucleotide, 3.34% tetranucleotide, 0.98% pentanucleotide and 0.71% hexanucleotide repeats. AG/CT repeat motifs were the most abundant, and GC/CG repeat motifs were somewhat rare, accounting for 54.16% and 2.69% of dinucleotide repeat motifs, respectively. A total of 365 SSR loci were obtained by 20 SSR primer pairs amplified in 20 clones of E. arundinaceus and its related species, and 188 SSR loci were specific to E. arundinaceus. Genetic similarity coefficient analysis by UPMGA methods clustered 20 clones of E. arundinaceus and its related species into two groups. Five clones of E. arundinaceus clustered separately with the remaining clones. These results may establish a foundation for further research investigating the E. arundinaceus genome and identifying genuine hybrids between sugarcane and E. arundinaceus.

Estimation of genetic diversity and population structure in Tinospora cordifolia using SSR markers.

Thirty polymorphic SSRs, derived from RNA sequencing of Tinospora cordifolia (willd.), were utilized for genetic diversity and population structure evaluation among 96 accessions collected from ten different geographical regions of India. A total of 7611 SSRs were identified from 268149 transcripts. Of all SSR loci, 69.07% of them were tri-nucleotide repeat motifs, followed by di-nucleotide repeat motifs (12.82%). A total of 230 alleles were generated by 30 SSRs with an average of 7.67 alleles per locus with comparatively higher polymorphic information content (average 0.68). The expected (He) and observed (Ho) heterozygosity means were 0.71 and 0.12, respectively. All the loci showed significant deviation from Hardy-Weinberg Equilibrium (HWE). The neighbor joining clustering based on jaccard's coefficient grouped all the 96 accessions into three major cluster which was also in congruence with model-based structure plot. The result of molecular variance (AMOVA) revealed higher genetic variance within populations than among populations. The result reflects an existence of high level of genetic diversity in the collected accessions of T. cordifolia. The accessions Tc131, Tc31, Tc129, Tc38, Tc16, Tc59, Tc60, Tc17, Tc106 and Tc130 was found to be potential and diverse in nature and the SSRs TCSSR-18, TCSSR-37, TCTSSR-59, TCTSSR-92, TCTSSR-123 and TCTSSR-126 as potential markers. These accessions and newly developed SSR markers provide valuable resource and could be strategically utilized for further genetic improvement of T. cordifolia.

Development and Evaluation of SSR Markers Based on Large Scale Full-Length Transcriptome Sequencing in Sugarcane

Sugarcane generates the vast majority of sugar consumed worldwide. The large-scale development of EST-SSR markers are crucial for the analysis of genetic mechanisms important in agronomic traits of sugarcane. In this study, based on published 107,598 full-length expressed sequence tags (ESTs) from 22 sugarcane cultivars, we identified a total of 46,043 loci of simple repeat sequences. The SSRs with di-nucleotide (8175 loci) and tri-nucleotide (10,709 loci) repeat motifs account for 40.96% (18,884) of the total SSR loci, with (AT/TA)n and (ACA/TGT)n being found to be the major repeat motifs. A total of 1070 pairs of primers were randomly selected to verify using 12 accessions including S. officinarum, S. robustum, S. spontaneum and cultivars. The results showed that 847 (79.1%) were successfully amplified, of which 349 (32.60%) were polymorphic in the analyzed samples. The polymorphic rates of EST-SSR markers with di-nucleotide, tri-nucleotide, tetra-nucleotide, penta-nucleotide and hexa-nucleotide repeat motifs were 36.82% (81), 49.40% (165), 43.04% (34), 30.19% (32) and 34.26% (37), respectively. Among them, the EST-SSRs comprising five types of repeat motifs (CA)n, (CCG)n, (CCGC)n, (CGGCG)n and (GCCGGC)n presented high degrees of polymorphism. Finally, 20 EST-SSR markers with polymorphisms were selected to perform a cluster analysis of 48 accessions from Saccharum and Erianthus genera. These results demonstrated that Chinese sugarcane cultivars from group IV (25/39) had a lower genetic divergence than cultivars from other countries and EST-SSR markers can also be used in determining the genetic diversity of Erianthus genus. This set of EST-SSR markers is an important molecular resource for analyzing genetic diversity, molecular fingerprinting and genetic mapping.

A Global Analysis of Y-STR INRA189 Polymorphism in Chinese Domestic Yak Breeds/Populations.

Simple SummaryY chromosome-specific markers have been widely used in studying the origin, migration, diversity, and population relationship in several mammalian species. So far, the investigations on yak paternal genetics were mostly based on Y-SNPs information, but very few on Y-STR markers. In this study, we comprehensively investigated the polymorphism of Y-STR INRA189 locus, identified the geographical distribution pattern of its alleles in 15 Chinese domestic yak breeds/populations, and provided basic data for yak paternal genetic analysis. Our results showed that INRA189 is an intermediate polymorphic Y-STR marker with six alleles present among 15 Chinese domestic yak breeds/populations and that the variation among six alleles was due to different numbers of repetitions of a TG dinucleotide motif.The objective of this study was to probe into the polymorphism of Y-STR INRA189 and identify the geographical distribution pattern of its alleles in the Chinese domestic yak gene pool. We examined the variation at INRA189 locus in 682 male yaks representing 15 breeds/populations in China. The results showed that six alleles, including five reported previously (149, 155, 157, 159, and 161 bp) and a new one identified in this study (139 bp), were detected at INRA189 locus based on genotyping analysis. The frequencies of six alleles varied among the 15 yak breeds/populations with a clear phylogeographical pattern, which revealed the paternal genetic difference among Chinese yak breeds/populations. The average polymorphism information content (PIC) among the 15 yak breeds/populations was 0.32, indicating INRA189 to be an intermediate polymorphic Y-STR marker (0.25 < PIC < 0.5) in yak. Sequence alignment revealed that the variations among six alleles at INRA189 were defined by a TG dinucleotide repeat motif, which repeated for 12, 17, 20, 21, 22, and 23 times, corresponding to the alleles of 139, 149, 155, 157, 159, and 161 bp, respectively. Therefore, we believe that the polymorphic yak Y-STR INRA189 can be used to characterize male-mediated genetic events, including paternal genetic origin, diversity, and evolution.

Development of Twenty-Six Novel Microsatellite Markers in Pampus argenteus (Perciformes: Stromateidae) and Cross-Species Amplification in Closely Related Species, Pampus minor

Pampus argenteus (Perciformes: Stromateidae) is an economically important benthopelagic fish, which is widely distributed along the coast of China, Indian Ocean, Arabian Gulf and North Sea. To benefit population genetics studies and resource management, 26 pairs of novel microsatellite loci of P. argenteus were isolated using combined biotin capture method. These loci all included di-nucleotide repeat motifs. All markers showed polymorphism when assessed in 30 individuals from Xiapu population. The number of alleles per locus (NA) ranged from 4 to 22, and polymorphism information content (PICs) were from 0.565 to 0.924. Mean values of observed (HO) and expected (HE) heterozygosities ranged from 0.267 to 1.000 and from 0.633 to 0.929, respectively. Cross-species amplification showed that 22 microsatellite markers were successfully amplified in 30 individuals of P. minor, a closely related species of P. argenteus, and indicated clearly polymorphisms. The markers developed in this study will provide a useful tool for investigating the genetic structure, gene flow, and mating system of P. argenteus and the closely related species. They will also facilitate study on their evolutionary responses to the ongoing coastal systems change.

Transcriptome landscaping for gene mining and SSR marker development in Coriander (Coriandrum sativum L.)

Coriander (Coriandrum sativum L.) is an aromatic herb, widely used as a spice and is of great pharmaceutical interest. Despite high medicinal and economic value, there is a dearth of genomic information about profiling as well as the expressed sequence-based genic markers. In this study, transcriptome was sequenced from seeds, leaves, and flower for gene mining and identification of SSR markers. A total of 9746 SSR containing loci were identified, the most abundant type of SSR identified were the di-nucleotide repeat motifs (45.5%), followed by tri- (34.6%), tetra- (4.5%), penta- (1.5%) and hexanucleotide repeats (1%). A total of 3795 primers were designed, out of which 120 randomly selected were validated in 14 accessions of coriander cultivated in India. The current study provides useful information about preliminary transcriptome sketch and genic markers, which can be useful in breeding and genetic diversity estimation of coriander.