Number Of Simple Sequence Repeats Research Articles

Comparative genomics on chloroplasts of Rubus (Rosaceae)

Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.

Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper

AbstractThe Arnaucho chili pepper (ACP) is a traditional vegetable used in Peru because of its gastronomic properties. Due to its importance in the Peruvian diet and economy, this species is a resource that can be a candidate to plant breeding programs. In this study, the complete genome nucleotide sequence of this chili pepper was generated using the Illumina Hiseq 2500 sequencing technology. We sequenced the whole genome of the ACP using a paired-end 150 strategy, obtaining 330.46 GB of sequencing data. The genome size of the ACP was 2.98 Gb with a contig N50 of 237 Mb and 95.39% complete BUSCOs. Also, we identified 71.96% of repetitive DNA of the genome assembly, of which retroelements occupy 37.95% of the total genome. We downloaded genomes of the Solanoideae subfamily and conducted a comparative analysis of simple sequence repeats (SSRs) with our draft genome, and we identified lower number of SSRs in the ACP genome compared to other pepper species. This first ACP genome is expected to contribute to a better understanding of its genetics to adapt to the arid conditions of the Peruvian coastal ecosystem and evolution.

The first complete chloroplast genome sequences of Pistacia eurycarpa Yalt, a horticultural important rootstock and industrial tree

AbstractPistacia genus is botanically classified in the Sapindales order and the Anacardiaceae family, and the member of this genus P. eurycarpa is used as a rootstock for pistachio. Due to its rich oil content, various soaps are produced from the green peels of P. eurycarpa nuts and are used in the cosmetic industry as soap. In the current study, we aimed to release the complete chloroplast genome of P. eurycarpa to detect the relationship of the members of the Sapindales and also Pistacia genus. The length of the chloroplast genome of P. eurycarpa was identified 160,693 (bp) and consisted of the distinct parts of the genomic fragments such as LSC, SSC, and IR regions. The length of the LSC was 88,410 (bp), and SSC genomic range represented a total of 19,087 (bp). Inverted regions length was 26,598 (bp). A total of 125 genes were determined within the whole chloroplast genome of P. eurycarpa. The number of simple sequence repeats (SSRs) in the chloroplast genome was computed as 74. Three main clusters defined the dendrogram of all accessions. The closest pairs of species were identified among the P. eurycarpa and P. vera species. The farthest genetic relationship was calculated among the members of the Sapindales species Mangifera indica and the Fagales species Castanea mollissima. The sequences of the chloroplast genome of P. eurycarpa species can be evaluated for the construction of the basis of the complete evolution of the order, genera, and the development of the SSRs for species-specific markers for revealing the evolution of Pistacia species for future breeding research.

Characterization of Simple Sequence Repeat (SSR) Markers Mined in Whole Grape Genomes.

SSR (simple sequence repeat) DNA markers are widely used for genotype DNA identification, QTL mapping, and analyzing genetic biodiversity. However, SSRs in grapes are still in their early stages, with a few primer pairs accessible. With the whole-genome sequencing (WGS) of several grape varieties, characterization of grape SSR changed to be necessary not only to genomics but to also help SSR development and utility. Based on this, we identified the whole-genome SSR of nine grape cultivars ('PN40024', 'Cabernet Sauvignon', 'Carménère', 'Chardonnay', 'Merlot', 'Riesling', 'Zinfandel', 'Shine Muscat', and 'Muscat Hamburg') with whole-genome sequences released publicly and found that there are great differences in the distribution of SSR loci in different varieties. According to the difference in genome size, the number of SSRs ranged from 267,385 (Cabernet Sauvignon) to 627,429 (Carménère), the density of the SSR locus in the genome of nine cultivars was generally 1 per Kb. SSR motif distribution characteristic analysis of these grape cultivars showed that the distribution patterns among grape cultivars were conservative, mainly enriched in A/T. However, there are some differences in motif types (especially tetranucleotides, pentanucleotides, and hexanucleotides), quantity, total length, and average length in different varieties, which might be related to the size of the assembled genome or the specificity of variety domestication. The distribution characteristics of SSRs were revealed by whole-genome analysis of simple repeats of grape varieties. In this study, 32 pairs of primers with lower polymorphism have been screened, which provided an important research foundation for the development of molecular markers of grape variety identification and the construction of linkage maps of important agronomic traits for crop improvement.

Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome.

The Aristolochia, as an important genus comprised of over 400 species, has attracted much interest because of its unique chemical and pharmacological properties. However, the intrageneric taxonomy and species identification within Aristolochia have long been difficult because of the complexity of their morphological variations and lack of high-resolution molecular markers. In this study, we sampled 11 species of Aristolochia collected from distinct habitats in China, and sequenced their complete chloroplast (cp) genomes. The 11 cp genomes of Aristolochia ranged in size from 159,375bp (A. tagala) to 160,626 bp (A. tubiflora), each containing a large single-copy (LSC) region (88,914-90,251 bp), a small single-copy (SSC) region (19,311-19,917 bp), and a pair of inverted repeats (IR) (25,175-25,698 bp). These cp genomes contained 130-131 genes each, including 85 protein-coding genes (CDS), 8 ribosomal RNA genes, and 37-38 transfer RNA genes. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in Aristolochia species. A. littoralis had the highest number of repeats (168), while A. tagala had the lowest number (42). The total number of simple sequence repeats (SSRs) is at least 99 in A. kwangsiensis, and, at most, 161 in A. gigantea. Interestingly, we detected eleven highly mutational hotspot regions, including six gene regions (clpP, matK, ndhF, psbT, rps16, trnK-UUU) and five intergenic spacer regions (ccsA-ndhD, psbZ-trnG-GCC, rpl33-rps18, rps16-trnQ-UUG, trnS-GCU-trnG-UCC). The phylogenetic analysis based on the 72 protein-coding genes showed that 11 Aristolochia species were divided into two clades which strongly supported the generic segregates of the subgenus Aristolochia and Siphisia. This research will provide the basis for the classification, identification, and phylogeny of medicinal plants of Aristolochiaceae.

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

BackgroundThe complex physical structure and abundant repeat sequences make it difficult to assemble the mitogenomes of seed plants, especially gymnosperms. Only approximately 33 mitogenomes of gymnosperms have been reported. However, as the most widely distributed and the second largest family among gymnosperms, Cupressaceae has only six assembled mitogenomes, including five draft mitogenomes and one complete mitogenome, which has greatly hindered the understanding of mitogenome evolution within this large family, even gymnosperms.ResultsIn this study, we assembled and validated the complete mitogenome of Thuja sutchuenensis, with a size of 2.4 Mb. Multiple sequence units constituted its complex structure, which can be reduced to three linear contigs and one small circular contig. The analysis of repeat sequences indicated that the numbers of simple sequence repeats increased during the evolutionary history of gymnosperms, and the mitogenome of Thuja sutchuenensis harboured abundant extra-long repeats (more than 5 kb). Additionally, the longest repeat sequence identified in these seven gymnosperms also came from the mitogenome of Thuja sutchuenensis, with a length of up to 47 kb. The analysis of colinear blocks and gene clusters both revealed that the orders of mitochondrial genes within gymnosperms was not conserved. The comparative analysis showed that only four tRNAs were shared by seven gymnosperms, namely, trnD-GUC, trnE-UUC, trnI-CAU and trnY-GUA. Furthermore, four genes have undergone potential positive selection in most gymnosperm species, namely, atp8, ccmB, mttB and sdh4.ConclusionWe successfully assembled the second complete mitogenome within Cupressaceae and verified that it consisted of multiple sequence units. Our study also indicated that abundant long repeats may contribute to the generation of the complex conformation of the mitogenome of Thuja sutchuenensis. The investigation of Thuja sutchuenensis’s mitogenome in our study provides new insight into further understanding the complex mitogenome architecture within gymnosperms.

Plastome evolution and phylogenomics of Impatiens (Balsaminaceae)

This study reported seven new plastomes from Impatiens and observed three highly variable regions for phylogeny and DNA barcoding, which resolved the relationships among sections of subgenus Impatiens. Impatiens L. (Balsaminaceae, Ericales) is one of the largest and most diverse genera of angiosperms, widely known for its taxonomic difficulty. In this study, we reevaluated the infrageneric relationships within the genus Impatiens, using complete plastome sequence data. Seven complete plastomes of Impatiens (representing 6 species) were newly sequenced and characterized along with 20 previously published plastomes of other Impatiens species, plus 2 plastomes of outgroups (Hydrocera triflora, Balsaminaceae; Marcgravia coriacea, Marcgraviaceae). The total size of these 29 plastomes ranged from 151,538bp to 152,917bp, except 2 samples of Impatiens morsei, which exhibited a shorter length and lost some genes encoding NADH dehydrogenase subunits. Moreover, the number of simple sequence repeats (SSRs) ranged from 51 to 113, and the number of long repeats from 17 to 26. In addition, three highly variable regions were identified (trnG-GCC (The previous one), ndhF-rpl32-trnL-UGA-ccsA, and ycf1). Our phylogenomic analysis based on 80 plastome-derived protein-coding genes strongly supported the monophyly of Impatiens and its two subgenera (Clavicarpa and Impatiens), and fully resolved relationships among the six (out of seven) sampled sections of subgenus Impatiens. Overall, the plastome DNA markers and phylogenetic results reported in this study will facilitate future identification, taxonomic and DNA barcoding studies in Impatiens as well as evolutionary studies in Balsaminaceae.

Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae).

Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F. sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 (F. dinganensis and F. howii) to 190 (F. polynervis), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes (accD, clpP, ndhK, rbcL, rpl20, rpl22, rpl23, rpoC1, rps15, and rps4) which exhibited potential positive selective signatures. Five hypervariable genic regions (rps15, ycf1, rpoA, ndhF, and rpl22) and five hypervariable intergenic regions (trnH-GUG-psbA, rpl32-trnL-UAG, psbZ-trnG-GCC, trnK-UUU-rps16 and ndhF-rpl32) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus, despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F. sarmentosa complex and F. auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.

The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species.

Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.

Plastid Phylogenomics of Paeonia and the Evolution of Ten Flower Types in Tree Peony.

Paeonia suffruticosa Andr., a member of Paeoniaceae, is native to China. In its 1600 years' cultivation, more than 2000 cultivars for different purposes (ornamental, medicinal and oil use) have been inbred. However, there are still some controversies regarding the provenance of tree peony cultivars and the phylogenetic relationships between and within different cultivar groups. In this study, plastid genome sequencing was performed on 10 representative tree peony cultivars corresponding to 10 different flower types. Structure and comparative analyses of the plastid genomes showed that the total lengths of the chloroplast genome of the 10 cultivars ranged from 152,153 to 152,385 bp and encoded 84-88 protein-coding genes, 8 rRNAs and 31-40 tRNAs. The number of simple sequence repeats and interspersed repeat sequences of the 10 cultivars ranged from 65-68 and 40-42, respectively. Plastid phylogenetic relationships of Paeonia species/cultivars were reconstructed incorporating data from our newly sequenced plastid genomes and 15 published species, and results showed that subsect. Vaginatae was the closest relative to the central plains cultivar group with robust support, and that it may be involved in the formation of the group. Paeonia ostii was recovered as a successive sister group to this lineage. Additionally, eleven morphological characteristics of flowers were mapped to the phylogenetic skeleton to reconstruct the evolutionary trajectory of flower architecture in Paeoniaceae.

Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences

Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.

Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari

Dracaena (Asparagaceae family) tree is famous for producing "dragon blood"—a bioactive red-colored resin. Despite its long history of use in traditional medicine, little knowledge exists on the genomic architecture, phylogenetic position, or evolution. Hence, in this study, we sequenced the whole chloroplast (cp) genomes of D. serrulata and D. cinnabari and performed comparative genomics of nine genomes of the genus Dracaena. The results showed that the genome sizes range from 155,055 (D. elliptica) to 155,449 (D. cochinchinensis). The cp genomes of D. serrulata and D. cinnabari encode 131 genes, each including 85 and 84 protein-coding genes, respectively. However, the D. hokouensis had the highest number of genes (133), with 85 protein coding genes. Similarly, about 80 and 82 repeats were identified in the cp genomes of D. serrulata and D. cinnabari, respectively, while the highest repeats (103) were detected in the cp genome of D. terniflora. The number of simple sequence repeats (SSRs) was 176 and 159 in D. serrulata and D. cinnabari cp genomes, respectively. Furthermore, the comparative analysis of complete cp genomes revealed high sequence similarity. However, some sequence divergences were observed in accD, matK, rpl16, rpoC2, and ycf1 genes and some intergenic spacers. The phylogenomic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, sister to the remaining Dracaena species sampled in this study, with high bootstrap values. In conclusion, this study provides valuable genetic information for studying the evolutionary relationships and population genetics of Dracaena, which is threatened in its conservation status.

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.

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions.

As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.

Comparative Analysis of Complete Chloroplast Genome and Phenotypic Characteristics of Japanese Apricot Accessions

Japanese apricot (Prunus mume Sieb. et Zucc.) is among the most valued fruits and flowering plants in eastern Asia. However, few comparative studies have been conducted with respect to its agro-morphological and pomological traits, chloroplast (cp) genome sequences and plastid diversity. Therefore, a comparative study was, conducted to investigate the divergence and geographic distribution of ten Japanese apricot accessions from three Chinese provinces (Zhejiang, Jiangsu and Sichuan). Phenotypic characteristics of the evaluated accessions, such as leaf length, tip leaf length, flower diameter, anther number, fruit weight, longitudinal height, transversal height, lateral height, fruit stone weight, stone longitudinal height, stone transversal height, stone lateral heigh, titratable acid content and total soluble solids, varied significantly (p < 0.05) among the ten investigated accessions. On the other hand, most of the investigated accessions were statistically similar within the same province. Comparing the Cp genomes of P. mume accessions with those of the genus Prunus revealed a similarity in structure and composition with slight differences. “Bayes empirical Bayes” (BEB) analysis in Prunus species, including P. mume, revealed BEB in rps16, rps3, rpoC1(4*), rpl32, rpl16, rbcL, psbF, petB, ndhF, clpP and ccsA genes. The BEB value of the rpoC1 gene is higher than 0.95, indicating that it is potentially under positive selection. Interestingly, the accessions from the same province of origin had the same number of forward repeat sequences. Furthermore, all accessions from Zhejiang province had the same number of simple sequence repeats. Similarly, nucleotide deletion/insertion of the ycf1 sequence and the results of phylogenetic trees revealed that accessions were mainly clustered according to their province of origin. Our comparative study of agronomical traits, chloroplast composition, structure, nucleotide variability of cp genome and phylogeography in Japanese apricot accessions provides valuable information on their diversity and geographic distribution.

The First Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Pistachio (Pistacia vera)

Pistachio is one of the most economically important nut crops worldwide. However, there are no reports describing the chloroplast genome of this important fruit tree. In this investigation, we assembled and characterized the complete pistachio chloroplast sequence. The Pistacia vera chloroplast genome was 160,598 bp in size, similar to other members of Anacardiaceae (149,011–172,199 bp) and exhibited the typical four section structure, including a large single copy region (88,174 bp), a small single copy region (19,330 bp), and a pair of inverted repeats regions (26,547 bp). The genome contains 121 genes comprised of 87 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Thirteen intron-containing genes were identified in the genome wherein two genes had more than two introns. The genomic patterns of GC content resembled those for other Anacardiaceae. P. vera displayed the highest number of simple sequence repeats (SSRs) among the genera studied, which may be useful for molecular marker development and future population studies. Amino acid analysis revealed that Leucine is the most frequent (10.69%) amino acid in the chloroplast genome followed by Isoleucine (8.53%) and Serine (7.77%). Cysteine (1.30%) and Tryptophan (1.74%) were the least frequent amino acids. Phylogenetic analysis revealed P. vera is most like its taxonomically close relative P. weinmaniifolia, followed by Rhus chinensis; all placed taxonomically in the tribe Rhoeae. Members of Anacardiaceae were most closely related to Rhoeae, followed by members of Spondieae. The reports of this chloroplast genome will be useful for future conservation studies, genetic evaluation and breeding of P. vera, and more comprehensive phylogenetic analysis of the Pistacia species and its closely-related genera.

Microsatellite Characteristics of Silver Carp (Hypophthalmichthysmolitrix) Genome and Genetic Diversity Analysis in Four Cultured Populations.

Hypophthalmichthys molitrix is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on H. molitrix genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs in the assembled H. molitrix genome were analyzed, and new markers were developed to preliminarily evaluate the genetic diversity of the four breeding populations. A total of 368,572 SSRs were identified from the H. molitrix genome. The total length of SSRs was 6,492,076 bp, accounting for 0.77% of the total length of the genome sequence. The total frequency and total density were 437.73 loci/Mb and 7713.16 bp/Mb, respectively. Among the 2–6 different nucleotide repeat types, SSRs were dominated by di-nucleotide repeats (204,873, 55.59%), and AC/GT was the most abundant motif. The number of SSRs on each chromosome was positively correlated with the length. The 13 pairs of markers developed were used to analyze the genetic diversity of four cultivated populations in Hubei Province. The results showed that the genetic diversity of the four populations was low, and the ranges of alleles (Na), effective alleles (Ne), observed heterozygosity (Ho), and Shannon’s index information (I) were 3.538–4.462, 2.045–2.461, 0.392–0.450, and 0.879–0.954, respectively. Genetic variation occurs mainly among individuals within populations (95.35%). UPGMA tree and Bayesian analysis showed that four populations could be divided into two different branches. Therefore, the genome-wide SSRs were effectively in genetic diversity analysis on H. molitrix.

MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.)

MIG-seq (Multiplexed inter-simple sequence repeats genotyping by sequencing) has been developed as a low cost genotyping technology, although the number of polymorphisms obtained is assumed to be minimal, resulting in the low application of this technique to analyses of agricultural plants. We applied MIG-seq to 12 plant species that include various crops and investigated the relationship between genome size and the number of bases that can be stably sequenced. The genome size and the number of loci, which can be sequenced by MIG-seq, are positively correlated. This is due to the linkage between genome size and the number of simple sequence repeats (SSRs) through the genome. The applicability of MIG-seq to population structure analysis, linkage mapping, and quantitative trait loci (QTL) analysis in wheat, which has a relatively large genome, was further evaluated. The results of population structure analysis for tetraploid wheat showed the differences among collection sites and subspecies, which agreed with previous findings. Additionally, in wheat biparental mapping populations, over 3,000 SNPs/indels with low deficiency were detected using MIG-seq, and the QTL analysis was able to detect recognized flowering-related genes. These results revealed the effectiveness of MIG-seq for genomic analysis of agricultural plants with large genomes, including wheat.

The Complete Mitogenome of Elymus sibiricus and Insights Into Its Evolutionary Pattern Based on Simple Repeat Sequences of Seed Plant Mitogenomes.

The most intriguing characteristics of plant mitochondrial genomes (mitogenomes) include their high variation in both sequence and structure, the extensive horizontal gene transfer (HGT), and the important role they play in hypoxic adaptation. However, the investigation of the mechanisms of hypoxic adaptation and HGT in plant mitochondria remains challenging due to the limited number of sequenced mitogenomes and non-coding nature of the transferred DNA. In this study, the mitogenome of Elymus sibiricus (Gramineae, Triticeae), a perennial grass species native to the Qinghai-Tibet plateau (QTP), was de novo assembled and compared with the mitogenomes of eight Gramineae species. The unique haplotype composition and higher TE content compared to three other Triticeae species may be attributed to the long-term high-altitude plateau adaptability of E. sibiricus. We aimed to discover the connection between mitogenome simple sequence repeats (SSRs) (mt-SSRs) and HGT. Therefore, we predicted and annotated the mt-SSRs of E. sibiricus along with the sequencing of 87 seed plants. The clustering result based on all of the predicted compound mitogenome SSRs (mt-c-SSRs) revealed an expected synteny within systematic taxa and also inter-taxa. The mt-c-SSRs were annotated to 11 genes, among which “(ATA)3agtcaagtcaag (AAT)3” occurred in the nad5 gene of 8 species. The above-mentioned results further confirmed the HGT of mitogenomes sequences even among distant species from the aspect of mt-c-SSRs. Two genes, nad4 and nad7, possessed a vast number of SSRs in their intron regions across the seed plant mitogenomes. Furthermore, five pairs of SSRs developed from the mitogenome of E. sibiricus could be considered as potential markers to distinguish between the species E. sibiricus and its related sympatric species E. nutans.

Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis.

Skeletonema species are cosmopolitan coastal diatoms that exhibit important roles in ecological system. The chloroplast genomes (cpDNAs) have been proven to be important in the study of molecular evolution and genetic diversity. However, cpDNA of only a single Skeletonema species (S. pseudocostatum) has been constructed, hindering in-depth investigation on Skeletonema species. In this study, complete cpDNAs of five Skeletonema species were constructed with cpDNAs of four species S. marinoi, S. tropicum, S. costatum, and S. grevillea constructed for the first time. These cpDNAs had similar sizes and same numbers of genes. These cpDNAs were highly syntenic with no substantial expansions, contractions, or inversions. Interestingly, two copies of petF, which encodes ferredoxin with critical role in iron dependency, were found in all five Skeletonema species, with one copy in the cpDNA and another copy in the nuclear genome of each species. Selection analysis revealed that all PCGs of cpDNAs were undergoing purifying selection. Despite the high conservation of these cpDNAs, nine genomic regions with high sequence divergence were identified, which illustrated substantial variations that could be used as markers for phylogenetic inference and for tracking Skeletonema species in the field. Additionally, the numbers of simple sequence repeats varied among different cpDNAs, which were useful for detecting genetic polymorphisms. The divergence times estimated using PCGs of cpDNAs revealed that most of these species were established within ∼33 Mya, consistent with that estimated using mtDNAs. Overall, the current study deepened our understanding about the molecular evolution of Skeletonema cpDNAs.