Phylogenetically clustering of rhizobia by genome structure:application to unclassified Rhizobium

Previous research reveals that the genome structures of rhizobial type strains and reference strains can reflect their phylogenetic relationships. In order to further explore the potential application of genome structure as a phylogenetic marker in rhizobial natural taxonomy, this study analyzed the genome structures of 29 unclassified nodule bacteria isolated from the root nodules of leguminous trees, Robinia sp., Dalbergia spp., and A lbizia spp. and 7 rhizobial reference strains by I-CeuI cleavage, then clustered these bacteria phylogenetically based on their genome structures and compared these clusters with those based on numerical taxonomy and 16S rDNA PCR-RFLP. Eleven phylogenetic clusters were obtained, The clusters were in large part consistent with those based on numerical taxonomy and 16S rDNA PCR-RFLP. Also there are inconsistent clusters based on the above three methods. But results are completely consistent with 16S rRNA clusters. This suggested that the genome structure clustering method can be used to lastly identify root nodule isolates and detect their phylogenetic relationships. The credibility and repeatability of the results, together with the simplicity and possibility to analyze a large number of strains in a short time of the method, indicates the broad potential application of genome structure as phylogenetic marker to categorize rhizobial isolates and should in the future facilitate biodiversity studies.

Characterization of the sequence spectrum of DNA based on the appearance frequency of the nucleotide sequences of the genome——A new method for analysis of genome structure

The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.

Toward Elucidating the Structure of Tetraploid Cotton Genome

Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evolutionary studies of the species.Here,we employed GeneTrek and

Comparative Analysis of the Exon-Intron Structure in Eukaryotic Genomes

The exon numbers and lengths vary in different eukaryotic species. With increasing completed genomic sequences, it is indispensable to reanalyze the gene organization in diverse eukaryotic genomes. We performed a large-scale comparative analysis of the exon-intron structure in 72 eukaryotic organisms, including plants, fungi and animals. We confirmed that the exon-intron structure varies massively among eukaryotic genomes and revealed some lineage-specific features of eukaryotic genes. These include a teleost-specific exon-intron structure pattern, relatively small introns and large exons in fungi and algae, and a gradual expansion of introns in vertebrates. Furthermore, the conservation analysis of exon-intron boundaries indicates that several bases near splice site junctions are different in introns with variable length among different species. After comparison, we identified a trend showing increases in intron densities and lengths in diverse species from fungi, plants, invertebrates to vertebrates, while it was the opposite in relation to exon lengths. The statistical properties of eukaryotic genomic organization suggest that genome-specific features are preserved by diverse evolutionary processes, which paves way for further research on the diversification of eukaryotic evolution.

Analysis on Genomic Structure Changes and Diversity of Introgression Lines in Dongxiang Wild Rice(Oryza rufipogon Griff.)

[Objective] The aim of the study was to make research on genomic struc- ture variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of Oryza rufipogon Griff. and receptor of O. sativa sp. indica Kate. Strains of 239 in the group were analyzed on Polymor- phism with the help of 25 couples of SSR primers distributed in 12 pairs of chromo- somes. [Result] Gene fragments of O. rufipogon Griff. were found penetrated in the 25 microsatellite sites and most of the groups kept the parents of Xieqinzao B or DNA sequence of O. rufipogon Griff. The average rate of recurrent homozygous bands was 78.13% in the ILs, but the highest was 94.98% （amplified by primer RM131） and the lowest was 60.25% （RM171）. The average rate of donor homozy- gous bands was 13.37%, but the highest was 32.64% （RM171） and the lowest was 2.93% （RM1095）. There were numerous heterozygous sites in the population and the average heterozygosis rate was 5.62%, while the highest was 10.04%（RM401）. Moreover, we found some parental fragments were lost and some novel fragments were not detected in either parent in BC1F6 population. The average rate of lost bands was 2.88%, while the highest was 13.39% （RM311） and the lowest was 0 （RM401）. The average rate of new bands was 1%. The average of Nei＇s gene di- versity （He） and Shannon＇s Information index （I） were 0.276 and 0.457 respectively in high generation of introgression lines. [Conclusion] The study demonstrated that distant hybridization led to extensive genetic and epigenetic variations in high gener- ation of introgression lines, which expanded the base of genetic variation and laid an important foundation for rice improvement and germplasm innovation.

Structural Variation Analysis of Mutated Nannochloropsis oceanica Caused by Zeocin Through Genome Re-Sequencing

Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.

The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.

Genomic structure analysis of SNC6, a progesterone-receptor associated protein gene, and cloning and characterization of its 5＇-flanking region

Objective: To analyze the genomic structure of SNC6, a progesterone\|receptor associated protein gene and its regulatory elements in its 5'\|flanking region. Methods: Genomic sequence from GenBank database (accession number: Z98048) covering the whole SNC6 gene was used to analyze the genomic structure of SNC6 and design primers for PCR amplification of its 5'\|flanking region. A 1894 bp fragment of the 5'\|flanking region \{(-1814\} to +75) was cloned by PCR using genomic DNA from a healthy donor peripheral blood lymphocyte as template. This fragment, as well as 3 shorter derivative fragments (1423 bp, 632 bp and 416 bp, which correspond to -1344 to +75, -552 to +75 and -337 to +75 respectively), were subcloned into pGL2 series luciferase reporter vectors. These constructs were introduced into colorectal cancer cell line SW620 for transient expression of reporter gene and luciferase activities were measured. Results: The genomic structure analysis showed there are 12 exons for SNC6 gene, which spans 32017 bp (nt71529 to nt39513 in Z98048 sequence). All transfected SW620 cells with the above 5\|flanking region\|containing constructs showed luciferase activities. The highest luciferase activities were measured in transfected cells with vectors containing 1894 bp fragments, and the lowest luciferase activities were measured in transfected cells with vectors containing 416 bp fragments. Luciferase activities were higher in transfected cells with vectors containing 632 bp fragments than that in transfected cells with vectors containing 1423 bp fragments. Conclusion: The basic transcription\|promoting element (promoter) for SNC6 expression resides between 0 to -337, and two transcription\|enhancing elements (enhancer) resides between -337 to -552 and -1344 to -1814, whereas one transcription\|inhibiting element (silencer) exists between -552 to -1344.

Structural features of the nucleotide sequences of virus and organelle genomes

The four nucleotides (bases), A, T (U), G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were also arranged sophisticatedly in the structural features in a single-strand with 1) reverse-complement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs. P (L) (the probability of the base-distribution at L), although their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic-and the eukaryotic cells. In the case of the genomic DNA composed of less than 10,000 nt, it was better than to be partitioned at 10 of the L-value, and the structural features for the biologically active genomic DNA were observed as the large genomes. As the results, the base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes. In addition, the relationship between the structural features of the genome and the biological complexity was discussed.

Sequence and organization of the mitochondrial genome of an urostylidid bug,Urochela quadrinotata Reuter(Hemiptera:Urostylididae)

The complete mitochondrial genome of Urochela quadrinotata Reuter was sequenced and analyzed. This represents the first sequence completed for an insect in the family Urostylididae. The genome is 16585 bp in size and contains 35 genes （including 13 protein-coding genes, 20 transfer RNA genes, two ribosomal RNAs and a control region） with an A＋T content of 75.4%. Two tRNA genes, tRNATle and tRNAGln, are not detected in this genome. The gene order is similar to that most commonly found in insects. All tRNAs possess the typical clover-leaf structure, except tRNASer（AGN）, in which the dihydrouridine （DHU） arm forms a simple loop. The secondary structure of rrnL consists of six structural domains and 43 helices, and the rrnS includes three structural domains and 27 helices. An obvious feature of the control region is the presence of 1652 bp long tandem repeat sequences comprising 16 tandem repeat units.

The role of genomic structural variation in the genetic improvement of polyploid crops

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.

Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis

Structural genomics (SG) is an international effort that aims at solving three-dimensional shapes of important biological macro-molecules with primary focus on proteins. One of the main bottlenecks in SG is the ability to produce dif-fraction quality crystals for X-ray crystallogra-phy based protein structure determination. SG pipelines allow for certain flexibility in target selection which motivates development of in- silico methods for sequence-based prediction/ assessment of the protein crystallization pro-pensity. We overview existing SG databanks that are used to derive these predictive models and we discuss analytical results concerning protein sequence properties that were discov-ered to correlate with the ability to form crystals. We also contrast and empirically compare mo- dern sequence-based predictors of crystalliza-tion propensity including OB-Score, ParCrys, XtalPred and CRYSTALP2. Our analysis shows that these methods provide useful and compli-mentary predictions. Although their average ac- curacy is similar at around 70%, we show that application of a simple majority-vote based en-semble improves accuracy to almost 74%. The best improvements are achieved by combining XtalPred with CRYSTALP2 while OB-Score and ParCrys methods overlap to a larger extend, although they still complement the other two predictors. We also demonstrate that 90% of the protein chains can be correctly predicted by at least one of these methods, which suggests that more accurate ensembles could be built in the future. We believe that current protein crystalli-zation propensity predictors could provide useful input for the target selection procedures utilized by the SG centers.

Genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River

The traditional medicinal plant,and endangered species Aristolochia delavayi(Aristolochiaceae)is an endemic species in China and occurs in the warm and dry areas along the Jinsha river.It is also a specific host of the larvae of Byasa daemonius,a vulnerable butterfly.In this study,15 pairs of polymorphic microsatellite primers of A.delavayi were designed and screened based on the Simple Sequence Repeats(SSR)loci found by using the results of genome skimming.Based on these 15 SSR markers,the genetic diversity and structure of 193 individuals from ten natural populations were analyzed in detail.In comparison to other endemic and endangered plants in the region,the population of A.delavayi possess a relatively high genetic diversity(He=0.550,I=1.112).AMOVA analysis showed that 68.4%of the total genetic diversity was within populations and 31.6%of the variation occurred among populations.There was a significant genetic differentiation among natural populations of A.delavayi detectable,with low gene flow(Nm=0.591).This might be attributed to geographical barriers and limited seed dispersal.To test the isolation by distance(IBD),we performed Mantel test,which showed a significant correlation between the geographic and genetic distances.In order to cope with the possible biases caused by IBD,we additionally performed Bayesian genetic cluster analyses and principal coordinate analysis(PCoA).The final cluster analysis revealed three groups with distinct geographical distribution.Habitat fragmentation and limited gene flow between these populations may be the main reasons for the current genetic structure.For conservation of this species,we suggest to divide its populations into three protection management units,with subsequent focus on the Yongsheng and Luquan populations which experienced a genetic bottleneck event in the past.

Genome-wide evolution of MAPKs family and their expression in response to bacterial infection in seahorse Hippocampus erectus

Seahorses have evolved many unique biological traits,including a male brood pouch,the absence of caudal and pelvic fins,and the lack of spleen and gut-associated lymphatic tissue.The mitogenactivated protein kinases(MAPKs)are known to be involved in various important biological processes including growth,differentiation,immunity,and stress responses.Therefore,we hypothesized that the adaptive evolution and expression of the MAPK gene family in seahorse may differ from those of other teleost species.We identified positive selection sites in the erk2,erk5,jnk1,and p38αMAPK genes of the lined seahorse Hippocampus erectus and tiger-tailed seahorse Hippocampus comes.A novel expression profile of MAPK cascade genes was found in seahorse larvae during the first day after birth based on the RNA-seq data of H.erectus,which refl ected vital signs of immune response to its parental immune system.The expression patterns of the four positively selected MAPK genes were analyzed following the bacterial challenge of Vibrio fortis,revealing their upregulation pattern in brood pouch and other immune tissues.This study enriched our knowledge of the evolution of the H.erectus MAPK subfamilies,and could help better understanding the functional role of MAPKs in teleosts.

Phylogeny of Trigonotis in China-with a special reference to its nutlet morphology and plastid genome

The genus Trigonotis comprises nearly 60 species mainly distributed in East and Southeast Asia.China has the largest number of Trigonotis species in the world,with a total of 44 species,of which 38 are endemic.Nutlet morphology is useful for the taxonomic delimitation of Trigonotis.However,there are still controversial circumscriptions of nutlet shape in some species.In previous studies,interspecies phylogenetic relationships were inferred using few DNA markers and very few taxa,which possibly led to erroneous or incomplete conclusions.In this study,the nutlet morphology of 39 Trigonotis taxa and the characteristics of 34 complete chloroplast genomes(29 taxa)were investigated and analyzed.Then,the phylogenetic relationships were discussed within this genus based on complete chloroplast genomes.To the best of our knowledge,this study is the first comprehensive analysis of nutlet morphology and complete chloroplast genome of Trigonotis.Based on nutlet morphology,Trigonotis can be divided into two groups:Group 1,hemispherical or oblique tetrahedron with carpopodiums,and Group 2,inverted tetrahedron without carpopodiums.The chloroplast genome of Trigonotis exhibited a typical quadripartite structure,including 84-86 protein-coding,37 transfer RNA,and 8 ribosomal RNA genes,with a total length of 147,247-148,986 bp.Genes in the junctions were well conserved in Trigonotis,similar to those in other Boraginaceae s.str.species.Furthermore,Trigonotis chloroplast genomes showed relatively high diversity,with more conserved genic regions than intergenic regions;in addition,we detected 14 hot spots(Pi>0.005)in non-coding regions.Phylogenetic analyses based on chloroplast genome data identified highly resolved relationships between Trigonotis species.Specifically,Trigonotis was divided into two clades with strong support:one clade included species with hemispherical or oblique tetrahedron nutlets with carpopodiums and bracts,whereas the other clade included species with inverted tetrahedron nutlets without carpopodiums or bracts.Our results may inform future taxonomic,phylogenetic,and evolutionary studies on Boraginaceae.

Genome assembly of KA105,a new resource for maize molecular breeding and genomic research

Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for breeding.Its pedigree showed genetic divergence from B73 and other lines in its pedigree.Comparison with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight disease.More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development.The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

The identification of presence/absence variants associated with the apparent differences of growth period structures between cultivated and wild soybeans

The cultivated soybean（Glycine max（L.） Merr.） was distinguished from its wild progenitor Glycine soja Sieb.＆ Zucc.in growth period structure,by a shorter vegetative phase（V）,a prolonged reproductive phase（R） and hence a larger R/V ratio.However,the genetic basis of the domestication of soybean from wild materials is unclear.Here,a panel of 123 cultivated and 97 wild accessions were genotyped using a set of 24 presence/absence variants（PAVs） while at the same time the materials were phenotyped with respect to flowering and maturity times at two trial sites located at very different latitudes.The major result of this study showed that variation at PAVs is informative for assessing patterns of genetic diversity in Glycine spp.The genotyping was largely consistent with the taxonomic status,although a few accessions were intermediate between the two major clades identified.Allelic diversity was much higher in the wild germplasm than in the cultivated materials.A significant domestication signal was detected at 11 of the PAVs at 0.01 level.In particular,this study has provided information for revealing the genetic basis of photoperiodism which was a prominent feature for the domestication of soybean.A significant marker-trait association with R/V ratio was detected at 14 of the PAVs,but stripping out population structure reduced this to three.These results will provide markers information for further finding of R/V related genes that can help to understand the domestication process and introgress novel genes in wild soybean to broaden the genetic base of modern soybean cultivars.

A Genome Wide Association Study for Longevity in Cattle

Longevity is regarded as the most important functional trait in cattle breeding with high economic value yet low heritability. In order to identify genomic regions associated with longevity, a genome wise association study was performed using data from 4887 Fleckvieh bulls and 33,556 SNPs after quality control. Single SNP regression was used for identification of important SNPs including eigenvectors as a means of correction for population structure. SNPs selected with a false discovery rate threshold of 0.05 and with local false discovery rate identified genomic regions associated with longevity which were subsequently cross checked with the National Center for Biotechnology Information (NCBI) database. This, to identify interesting genes in cattle and their homologue forms in other species. The most notable genes were SYT10 located on chromosome 5, ADAMTS3 on chromosome 6, NTRK2 on chromosome 8 and SNTG1 on chromosome 14 of the cattle genome. Several of the genes found have previously been associated with cattle fertility. Poor fertility is an important culling reason and thereby affects longevity in cattle. Several signals were located in regions sparse with described genes, which suggest that there might be several other non-identified genetic pathways for this important trait.

Genome-wide association of 10 horticultural traits with expressed sequence tag-derived SNP markers in a collection of lettuce lines

Genetic diversity, population structure, and genome-wide marker-trait association analyses were conducted on a special collection of 298 homozygous lettuce(Lactuca sativa L.) lines. Each of these lines was derived from a single plant that had been genotyped with 384 SNP markers using LSGermOPA. They included 122 butterhead, 53 romaine, 63 crisphead, 53 leaf and 7 stem types. Genetic diversity among these plants was assessed by pairwise comparison based on 322 high-quality SNP markers selected from 384 SNPs. Only 258 unique genotypes were identified among the 298 lines because 26 pairs or small groups(a total of 66 lines) shared identical genotypes. The average genetic similarity coefficient(GS) among these unique genotypes was 63.9% with a range of 40.6% to 99.8%. A phylogenetic tree was constructed based on the genotypic data. The most likely number of populations was estimated to be two or six. Association analysis between the 322 SNP markers and 10 phenotypic traits using the 258 homozygous lines was performed by three different methods: single factor analysis, general linear model analysis, and mixed linear model analysis. Nine significant marker-trait associations(SMTAs) were detected at P < 0.0001 with all three methods and also when considering kinship and/or population structure for this collection, with five SMTAs for seed coat color, one for leaf undulation, two for leaf anthocyanin, and one for stem anthocyanin. These markers will be useful in marker-assisted selection after further validation with segregating populations.

The first complete organellar genomes of an Antarctic red alga,Pyropia endiviifolia:insights into its genome architecture and phylogenetic position within genus Pyropia(Bangiales,Rhodophyta)

Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes(ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina platform. The plastid genome(195 784 bp, 33.28% GC content) contains 210 protein-coding genes, 37 tRNA genes and 6 rRNA genes. The mitochondrial genome(34 603 bp, 30.5% GC content) contains 26 protein-coding genes, 25 tRNA genes and 2 rRNA genes. Our results suggest that the organellar genomes of Py. endiviifolia have a compact organization. Although the collinearity of these genomes is conserved compared with other Pyropia species, the genome sizes show significant differences, mainly because of the different copy numbers of rDNA operons in the pt DNA and group II introns in the mtDNA. The other Pyropia species have 2–3 distinct intronic ORFs in their cox 1 genes, but Py. endiviifolia has no introns in its cox 1 gene. This has led to a smaller mtDNA than in other Pyropia species. The phylogenetic relationships within Pyropia were examined using concatenated gene sets from most of the available organellar genomes with both the maximum likelihood and Bayesian methods. The analysis revealed a sister taxa affiliation between the Antarctic species Py. endiviifolia and the North American species Py. kanakaensis.