De novo assembly and analysis of Sonneratia ovata genome and population analysis

Mangroves are an important part of coastal and estuarine ecosystems where they serve as nurseries for marine species and prevent coastal erosion. Here we report the genome of Sonneratia ovata, which is a true mangrove that grows in estuarine environments and can tolerate moderate salt exposure. We sequenced the S. ovata genome and assembled it into chromosome-level scaffolds through the use of Hi-C. The genome is 212.3 Mb and contains 12 chromosomes that range in size from 12.2 to 23.2 Mb. Annotation identified 29,829 genes with a BUSCO completeness of 95.9%. We identified salt genes and found copy number expansion of salt genes such as ADP-ribosylation factor 1, and elongation factor 1-alpha. Population analysis identified a low level of genetic variation and a lack of population structure within S. ovata.

Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures

The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs' genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.

Adaptation of African swine fever virus to MA-104 cells: Implications of unique genetic variations

African swine fever virus (ASFV) is a large, double-stranded DNA virus that causes a fatal, contagious disease specifically in pigs. However, prevention and control of ASFV outbreaks have been hampered by the lack of an effective vaccine or antiviral treatment for ASFV. Although ASFV has been reported to adapt to a variety of continuous cell lines, the phenotypic and genetic changes associated with ASFV adaptation to MA-104 cells remain poorly understood. Here, we adapted ASFV field isolates to efficiently propagate through serial viral passages in MA-104 cells. The adapted ASFV strain developed a pronounced cytopathic effect and robust infection in MA-104 cells. Interestingly, the adapted variant maintained its tropism in primary porcine kidney macrophages. Whole genome analysis of the adapted virus revealed unique gene deletions in the left and right variable regions of the viral genome compared to other previously reported cell culture-adapted ASFV strains. Notably, gene duplications at the 5' and 3' ends of the viral genome were in reverse complementary alignment with their paralogs. Single point mutations in protein-coding genes and intergenic regions were also observed in the viral genome. Collectively, our results shed light on the significance of these unique genetic changes during adaptation, which facilitate the growth of ASFV in MA-104 cells.

A de novo chromosome-scale assembly of the Lablab purpureus genome

Introduction

Lablab (Lablab purpureus (L.) Sweet), an underutilized tropical legume crop, plays a crucial role in global food and nutritional security. To enhance our understanding of its genetic makeup towards developing elite cultivars, we sequenced and assembled a draft genome of L. purpureus accession PK2022T020 using a single tube long fragment read (stLFR) technique.

Results and discussion

The preliminary assembly encompassed 367 Mb with a scaffold N50 of 4.3 Mb. To improve the contiguity of our draft genome, we employed a chromatin contact mapping (Hi-C) approach to obtain a pseudochromosome-level assembly containing 366 Mb with an N50 length of 31.1 Mb. A total of 327.4 Mb had successfully been anchored into 11 pseudomolecules, corresponding to the haploid chromosome number in lablab. Our gene prediction recovered 98.4% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Comparative analyses utilizing sequence information from single-copy orthologous genes demonstrated that L. purpureus diverged from the last common ancestor of the Phaseolus/Vigna species approximately 27.7 million years ago. A gene family expansion analysis revealed a significant expansion of genes involved in responses to biotic and abiotic stresses. Our high-quality chromosome-scale reference assembly provides an invaluable genomic resource for lablab genetic improvement and future comparative genomics studies among legume species.

A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane

Background

Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations.

Methods

After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model.

Results

The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10-6 to 4.35 × 10-2, as well as some cane yield component traits with p values of 1.61 × 10-4 to 3.35 × 10-2. The significant association is consistent across four environments.

Conclusion

Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This marker is a high potential functional marker that may be used in sugarcane breeding programs to select superior sugarcane with good fiber and high sugar contents.

Comparative genomics and genome-wide SNPs of endangered Eld's deer provide breeder selection for inbreeding avoidance

Eld's deer, a conserved wildlife species of Thailand, is facing inbreeding depression, particularly in the captive Siamese Eld's deer (SED) subspecies. In this study, we constructed genomes of a male SED and a male Burmese Eld's deer (BED), and used genome-wide single nucleotide polymorphisms to evaluate the genetic purity and the inbreeding status of 35 SED and 49 BED with limited pedigree information. The results show that these subspecies diverged approximately 1.26 million years ago. All SED were found to be purebred. A low proportion of admixed SED genetic material was observed in some BED individuals. Six potential breeders from male SED with no genetic relation to any female SED and three purebred male BED with no relation to more than 10 purebred female BED were identified. This study provides valuable insights about Eld's deer populations and appropriate breeder selection in efforts to repopulate this endangered species while avoiding inbreeding.

The complete chloroplast genome sequence and phylogenetic analysis of Heritiera fomes Buch.-Ham. (Malvales: Sterculiaceae)

Heritiera fomes Buch.-Ham. (1800) is a species of mangrove in the family Malvaceae, widely distributed in the Indo-Pacific and listed as 'endangered' (EN) on the International Union for Conservation of Nature's (IUCN) red list. We reported the complete chloroplast genome sequence of H. fomes. The genome was 168,521 bp in length and included two inverted repeats (IRs) of 34,496 bp, separated by a large single-copy (LSC) region of 88,604 bp and a small single-copy (SSC) region of 10,925 bp, respectively. The genome contained 87 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The maximum-likelihood (ML) phylogenetic tree suggested that H. fomes is closely related to Heritiera angustata and Heritiera parvifolia with relatively high support bootstrap values of 86% and 100% with other species (Heritiera littoralis and Heritiera javanica), suggesting a relatively close genetic relationship between the five Heritiera plants. The chloroplast genome sequence provided a useful resource for conservation genetics studies of H. fomes and for phylogenetic studies of Heritiera.

Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand

Unique and biodiverse, mangrove ecosystems provide humans with benefits and contribute to coastal protection. Rhizophora mucronata, a member of the Rhizophoraceae family, is prevalent in the mangrove forests of Thailand. R. mucronata's population structure and genetic diversity have received scant attention. Here, we sequenced the entire genome of R. mucronata using 10× Genomics technology and obtained an assembly size of 219 Mb with the N50 length of 542,540 bases. Using 2857 single nucleotide polymorphism (SNP) markers, this study investigated the genetic diversity and population structure of 80 R. mucronata accessions obtained from the mangrove forests in Thailand. The genetic diversity of R. mucronata was moderate (I = 0.573, Ho = 0.619, He = 0.391). Two subpopulations were observed and confirmed from both population structure and principal component analysis (PCA). Analysis of molecular variance (AMOVA) showed that there was more variation within populations than between them. Mean pairwise genetic differentiation (FST = 0.09) showed that there was not much genetic difference between populations. Intriguingly, the predominant clustering pattern in the R. mucronata population did not correspond to the Gulf of Thailand and the Andaman Sea, which are separated by the Malay Peninsula. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. This research will provide important information for the future conservation and management of R. mucronata in Thailand.

Resequencing of durian genomes reveals large genetic variations among different cultivars

Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.

Genotyping by Sequencing (GBS) for Genome-Wide SNP Identification in Plants

Marker-assisted selection has played a pivotal role in developing several elite varieties in the past two decades. Molecular markers employed in plant breeding programs have recently shifted from microsatellites or simple sequence repeats (SSRs) to single nucleotide polymorphisms (SNPs) due to the ubiquity of SNP markers in the genome and the availability of various high-throughput SNP genotyping platforms. Rapid advances in sequencing technologies and the reduction in sequencing cost have facilitated SNP discovery in several plant species including non-model organisms with little or no genomic resources. Despite the lower cost of sequencing, genome complexity reduction approaches are still useful for SNP identification because many applications do not require every base of the genome to be sequenced. Genotyping-by-sequencing (GBS) is a quick and affordable reduced representation method that can simultaneously identify and genotype a large number of SNPs that has been successfully applied to a wide range of plant species. This chapter describes a robust two-enzyme GBS method for SNP discovery and genotyping that has been verified in non-model plant species.

Genome assemblies of Vigna reflexo-pilosa (créole bean) and its progenitors, Vigna hirtella and Vigna trinervia, revealed homoeolog expression bias and expression-level dominance in the allotetraploid

Vigna reflexo-pilosa (créole bean) is a wild legume belonging to the subgenus Ceratoropis and is widely distributed in Asia. Créole bean is the only tetraploid species in the genus Vigna, and it has been shown to derive from the hybridization of Vigna hirtella and Vigna trinervia. In this study, we combined the long-read PacBio technology with the chromatin contact mapping (Hi-C) technique to obtain a chromosome-level assembly of V. reflexo-pilosa. The final assembly contained 998,724,903 bases with an N50 length of 42,545,650 bases. Our gene prediction recovered 99.4% of the highly conserved orthologs based on the BUSCO analysis. To investigate homoeolog expression bias and expression level dominance in the tetraploid, we also sequenced and assembled the genomes of its progenitors. Overall, the majority of the homoeolog pairs (72.9%) displayed no expression bias, and among those that exhibited biased expression, 16.3% showed unbalanced homoeolog expression bias toward the V. trinervia subgenome. Moreover, 41.2% and 36.2% of the expressed gene pairs exhibited transgressive expression and expression level dominance, respectively. Interestingly, the genome-wide expression level dominance in the tetraploid was biased toward the V. trinervia subgenome. The analysis of methylation patterns also revealed that the average methylation levels in coding regions were higher in the V. hirtella subgenome than those in the V. trinervia subgenome. The genomic/transcriptomic resources for these three species are useful not only for the development of elite cultivars in Vigna breeding programs but also to researchers studying comparative genomics and investigating genomic/epigenomic changes following polyploid events.

A draft chromosome-scale genome assembly of a commercial sugarcane

Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum, S. spontaneum, and several other Saccharum species, resulting in an auto-allopolyploid with 8-12 copies of each chromosome. The current genome assembly gold standard is to generate a long read assembly followed by chromatin conformation capture sequencing to scaffold. We used the PacBio RSII and chromatin conformation capture sequencing to sequence and assemble the genome of a South East Asian commercial sugarcane cultivar, known as Khon Kaen 3. The Khon Kaen 3 genome assembled into 104,477 contigs totalling 7 Gb, which scaffolded into 56 pseudochromosomes containing 5.2 Gb of sequence. Genome annotation produced 242,406 genes from 30,927 orthogroups. Aligning the Khon Kaen 3 genome sequence to S. officinarum and S. spontaneum revealed a high level of apparent recombination, indicating a chimeric assembly. This assembly error is explained by high nucleotide identity between S. officinarum and S. spontaneum, where 91.8% of S. spontaneum aligns to S. officinarum at 94% identity. Thus, the subgenomes of commercial sugarcane are so similar that using short reads to correct long PacBio reads produced chimeric long reads. Future attempts to sequence sugarcane must take this information into account.

The complete chloroplast genome sequence of Intsia bijuga (Colebr.) Kuntze (Fabaceae: Detaroideae: Afzelieae)

Intsia bijuga (Colebr.) Kuntze. (1891) is a threatened mangrove species, belonging to the Fabaceae family and is native to the western Pacific coast and Southeast Asia. Here, we applied short-read Illumina technology to sequence and assemble its chloroplast genome. The complete chloroplast genome is 158,363 bp in length, composed of one large single-copy (LSC) region of 87,489 bp, one small single-copy (SSC) region of 19,438 bp, and a pair of inverted repeats (IRs) of 25,719 bp. A total of 129 unique genes were annotated, comprising 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Our phylogenetic analysis showed the placement of I. bijuga (OL699920.1) with Afzelia species within Fabaceae family.

A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand

Mitragyna speciosa (Kratom) is a tropical narcotic plant native to Southeast Asia with unique pharmacological properties. Here, we report the first chromosome-scale assembly of the M. speciosa genome. We employed PacBio sequencing to obtain a preliminary assembly, which was subsequently scaffolded using the chromatin contact mapping technique (Hi-C) into 22 pseudomolecules. The final assembly was 692 Mb with a scaffold N50 of 26 Mb. We annotated a total of 39,708 protein-coding genes, and our gene predictions recovered 98.4% of the highly conserved orthologs based on the BUSCO analysis. The phylogenetic analysis revealed that M. speciosa diverged from the last common ancestors of Coffea arabica and Coffea canephora approximately 47.6 million years ago. Our analysis of the sequence divergence at fourfold-degenerate sites from orthologous gene pairs provided evidence supporting a genome-wide duplication in M. speciosa, agreeing with the report that members of the genus Mitragyna are tetraploid. The STRUCTURE and principal component analyses demonstrated that the 85 M. speciosa accessions included in this study were an admixture of two subpopulations. The availability of our high-quality chromosome-level genome assembly and the transcriptomic resources will be useful for future studies on the alkaloid biosynthesis pathway, as well as comparative phylogenetic studies in Mitragyna and related species.

Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea

Bats (Chiroptera) constitute the second largest order of mammals and have several distinctive features, such as true self-powered flight and strong immunity. The Pendlebury's roundleaf bat, Hipposideros pendleburyi, is endemic to Thailand and listed as a vulnerable species. We employed the 10× Genomics linked-read technology to obtain a genome assembly of H. pendleburyi. The assembly size was 2.17 Gb with a scaffold N50 length of 15,398,518 bases. Our phylogenetic analysis placed H. pendleburyi within the rhinolophoid clade of the suborder Yinpterochiroptera. A synteny analysis showed that H. pendleburyi shared conserved chromosome segments (up to 105 Mb) with Rhinolophus ferrumequinum and Phyllostomus discolor albeit having different chromosome numbers and belonging different families. We found positive selection signals in genes involved in inflammation, spermatogenesis and Wnt signalling. The analyses of transposable elements suggested the contraction of short interspersed nuclear elements (SINEs) and the accumulation of young mariner DNA transposons in the analysed hipposiderids. Distinct mariners were likely horizontally transferred to hipposiderid genomes over the evolution of this family. The lineage-specific profiles of SINEs and mariners might involve in the evolution of hipposiderids and be associated with the phylogenetic separations of these bats from other bat families.

The complete chloroplast genome of Sonneratia griffithii Kurz (Lythraceae)

Sonneratia griffithii Kurz is a critically endangered mangrove species that can be found along the western coast of Thailand. In this study, we reported the complete chloroplast genome of S. griffithii. The chloroplast genome is 152,730 bp, consisting of one large single-copy (LSC) region, one small single-copy (SSC) region and a pair of inverted repeats (IRs). The LSC, SSC, and IR lengths are 87,226, 17,764, and 23,870 bp, respectively. The genome contains 113 unique genes, including 79 protein-coding, 30 tRNA, and 4 rRNA genes. The GC content of the chloroplast genome is 37.31%. The phylogenetic analysis based on 76 protein-coding genes showed a monophyletic group of S. griffithii and other Sonneratia species.

Chromosome-level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome-wide duplication event predating the divergence of Rhizophoraceae mangrove species

Mangrove ecosystems are unique, highly diverse, provide benefits to humans, and aid in coastal protection. The Indian mangrove, or spurred mangrove, [Ceriops tagal (Perr.) C. B. Rob.] is a member of the Rhizophoraceae family and is commonly found along the intertidal zones in tropical regions in Southeast Asia, southern Asia, and Africa. Here, we present the first high-quality reference genome assembly of the Ceriops species. A preliminary draft assembly, generated from the 10× Genomics linked-read library, was scaffolded using the proximity ligation chromatin contact mapping technique (Hi-C) to obtain a chromosome-scale assembly of 231,919,005 bases with an N50 length of 11,408,429 bases. The benchmarking universal single-copy orthologs (BUSCO) analysis revealed that C. tagal gene predictions recovered 95.8% of the highly conserved orthologs. Phylogenetic analyses suggested that C. tagal diverged from the last common ancestor of flat-leaf spurred mangrove [C. decandra (Griff.) Ding Hou] and C. zippeliana Blume ∼10.4 million yr ago (MYA), and the last common ancestor of genera Ceriops, Kandelia, and Rhizophora diverged from that of genus Bruguiera ∼49.4 MYA. In addition, our analysis of the transversion rate at fourfold-degenerate sites from orthologous gene pairs provided evidence supporting a recent whole-genome duplication in C. tagal. The STRUCTURE and principal component analyses illustrated that C. tagal individuals investigated in this study were the admixture of two subpopulations, the genetic background of which was influenced primarily by location. The availability of genomic and transcriptomic resources and biodiversity data reported in this work will be useful for future studies that may shed light on adaptive evolutions of mangrove species.

The complete mitochondrial genome sequence of the karst-dwelling crab, Terrapotamon thungwa (Crustacea: Brachyura: Potamidae)

Terrapotamon thungwa is a new species of terrestrial long-legged crab discovered in a karst landscape of southern Thailand. Here, we report the first complete mitochondrial genome of this crab species. The mitochondrial genome size is 16,156 base-pairs (bp), including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA) genes. The AT and GC content of the mitochondrial genome sequence is 73.2% and 26.8%, respectively. Phylogenetic analysis with 26 crustacean species, based on 13 mitochondrial conserve genes, showed that T. thungwa was closely related to other freshwater crab species in the family Potamidae.

Assembly of a hybrid mangrove, Bruguiera hainesii, and its two ancestral contributors, Bruguiera cylindrica and Bruguiera gymnorhiza

Mangroves are plants that live in tropical and subtropical coastal regions of the world, they are adapted to high salt environments and cyclic tidal flooding. Mangroves play important ecological roles, including acting as breeding grounds for many fish species and to prevent coastal erosion. The genomes of three mangrove species, Bruguiera gymnorhiza, Bruguiera cylindrica, and a hybrid of the two, Bruguiera hainesii were sequenced, assembled and annotated. The two progenitor species, B. gymnorhiza and B. cylindrica, were found to be highly similar to each other and sufficiently similar to B. parviflora to allow it to be used for reference based scaffolding to generate chromosome level scaffolds. The two subgenomes of B. hainesii were independently assembled and scaffolded. Analysis of B. hainesii confirms that it is a hybrid and the hybridisation event was estimated at 2.4 to 3.5 million years ago using a Bayesian Relaxed Molecular Clock approach.

A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome

Mangroves are of great ecological and economical importance, providing shelters for a wide range of species and nursery habitats for commercially important marine species. Ceriops zippeliana (yellow mangrove) belongs to Rhizophoraceae family and is commonly distributed in the tropical and subtropical coastal communities. In this study, we present a high-quality assembly of the C. zippeliana genome. We constructed an initial draft assembly of 240,139,412 bases with an N50 contig length of 564,761 bases using the 10x Genomics linked-read technology. This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related Ceriops species as a reference. The final assembly contained 243,228,612 bases with an N50 scaffold length of 10,559,178 Mb. The size of the final assembly was close to those estimated using DNA flow cytometry (248 Mb) and the k-mer distribution analysis (246 Mb). We predicted a total of 23,474 gene models and 21,724 protein-coding genes in the C. zippeliana genome, of which 16,002 were assigned gene ontology terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs analysis. The phylogenetic analysis based on single-copy orthologous genes illustrated that C. zippeliana and Ceriops tagal diverged approximately 10.2 million years ago (MYA), and their last common ancestor and Kandelia obovata diverged approximately 29.9 MYA. The high-quality assembly of C. zippeliana presented in this work provides a useful genomic resource for studying mangroves' unique adaptations to stressful intertidal habitats and for developing sustainable mangrove forest restoration and conservation programs.

A SNP variation in an expansin (EgExp4) gene affects height in oil palm

Oil palm (Elaeis guineensis Jacq.), an Aracaceae family plant, is utilized for both consumable and non-consumable products, including cooking oil, cosmetics and biodiesel production. Oil palm is a perennial tree with 25 years of optimal harvesting time and a height of up to 18 m. However, harvesting of oil palm fruit bunches with heights of more than 2-3 meters is challenging for oil palm farmers. Thus, understanding the genetic control of height would be beneficial for using gene-based markers to speed up oil palm breeding programs to select semi-dwarf oil palm varieties. This study aims to identify Insertion/Deletions (InDels) and single nucleotide polymorphisms (SNPs) of five height-related genes, including EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4, in short and tall oil palm groups by PacBio SMRT sequencing technology. Then, the SNP variation's association with height was validated in the Golden Tenera (GT) population. All targeted genes were successfully amplified by two rounds of PCR amplification with expected sizes that ranged from 2,516 to 3,015 base pair (bp), covering 5' UTR, gene sequences and 3' UTR from 20 short and 20 tall oil palm trees. As a result, 1,166, 909, 1,494, 387 and 5,384 full-length genomic DNA sequences were revealed by PacBio SMRT sequencing technology, from EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4 genes, respectively. Twelve variations, including eight InDels and four SNPs, were identified from EgDELLA1, EgGRF1, EgGA20ox1 and EgExp4. No variation was found for EgAPG1. After SNP through-put genotyping of 4 targeted SNP markers was done by PACE™ SNP genotyping, the association with height was determined in the GT population. Only the mEgExp4_SNP118 marker, designed from EgExp4 gene, was found to associate with height in 2 of 4 height-recordings, with p values of 0.0383 for height (HT)-1 and 0.0263 for HT-4. In conclusion, this marker is a potential gene-based marker that may be used in oil palm breeding programs for selecting semi-dwarf oil palm varieties in the near future.

Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests

Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.

The First Genetic Linkage Map of Winged Bean [Psophocarpus tetragonolobus (L.) DC.] and QTL Mapping for Flower-, Pod-, and Seed-Related Traits

Winged bean [Psophocarpus tetragonolobus (L.) DC.] (2n = 2× = 18) is a tropical legume crop with multipurpose usages. Recently, the winged bean has regained attention from scientists as a food protein source. Currently, there is no breeding program for winged bean cultivars. All winged bean cultivars are landraces or selections from landraces. Molecular markers and genetic linkage maps are pre-requisites for molecular plant breeding. The aim of this study was to develop a high-density linkage map and identify quantitative trait loci (QTLs) for pod and seed-related traits of the winged bean. An F₂ population of 86 plants was developed from a cross between winged bean accessions W054 and TPT9 showing contrasting pod length, and pod, flower and seed colors. A genetic linkage map of 1384 single nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing was constructed. The map resolved nine haploid chromosomes of the winged bean and spanned the cumulative length of 4552.8 cM with the number of SNPs per linkage ranging from 36 to 218 with an average of 153.78. QTL analysis in the F₂ population revealed 31 QTLs controlling pod length, pod color, pod anthocyanin content, flower color, and seed color. The number of QTLs per trait varied between 1 (seed length) to 7 (banner color). Interestingly, the major QTLs for pod color, anthocyanin content, and calyx color, and for seed color and flower wing color were located at the same position. The high-density linkage map QTLs reported in this study will be useful for molecular breeding of winged beans.

De novo reference assembly of the upriver orange mangrove (Bruguiera sexangula) genome

Upriver orange mangrove (Bruguiera sexangula) is a member of the most mangrove-rich taxon (Rhizophoraceae family) and is commonly distributed in the intertidal zones in tropical and subtropical latitudes. In this study, we employed the 10× Genomics linked-read technology to obtain a preliminary de novo assembly of the B. sexangula genome, which was further scaffolded to a pseudomolecule level using the Bruguiera parviflora genome as a reference. The final assembly of the B. sexangula genome contained 260 Mb with an N50 scaffold length of 11,020,310 bases. The assembly comprised 18 pseudomolecules (corresponding to the haploid chromosome number in B. sexangula), covering 204,645,832 bases or 78.6% of the 260-Mb assembly. We predicted a total of 23,978 protein-coding sequences, 17,598 of which were associated with gene ontology terms. Our gene prediction recovered 96.6% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. The chromosome-level assembly presented in this work provides a valuable genetic resource to help strengthen our understanding of mangroves’ physiological and morphological adaptations to the intertidal zones.

The complete mitochondrial genome of the Hipposideros pendleburyi (Pendlebury's leaf-nosed bat) an endemic species in Thailand

This study presents the first complete mitochondrial genome of the Hipposideros pendleburyi (Pendlebury's leaf-nosed bat), an endemic species in Thailand. The mitochondrial genome was 16,820 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The overall base composition was 31.5% A, 26.2% T, 28.3% C, and 14.0% G. A maximum-likelihood tree revealed that H. pendleburyi was grouped with Hipposideros armiger within the Hipposideridae clade, which has Rhinolophidae as a sister clade.

The complete mitogenome of the Thai soldier crab Mictyris thailandensis Davie, Wisespongpand & Shih, 2013 (Crustacea: Decapoda: Mictyridae)

Mictyris thailandensis has been described recently in the family Mictyridae which is found only in the Andaman Sea, west coast of Thailand. In this study, we performed shotgun genome sequencing of a male M. thailandensis using a paired-end (150 bp) sequencing chemistry on MGISEQ-2000RS and report the complete mitochondrial genome of M. thailandensis (15,557 bp). A total of 37 genes have been annotated: 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. Comparative phylogenetic analysis with 29 crustaceans based on 13 conserved genes demonstrated that M. thailandensis is closely related to other soldier crabs in the family Mictyridae. The mitogenome of M. thailandensis presented here provides useful genetic information to help understand the evolutionary relationships among the Mictyridae family members.

The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses

Fungi are rich in complexes of cryptic species that need a combination of different approaches to be delimited, including genomic information. Beauveria (Cordycipitaceae, Hypocreales) is a well-known genus of entomopathogenic fungi, used as a biocontrol agent. In this study we present a polyphasic taxonomy regarding two widely distributed complexes of Beauveria: B. asiatica and B. bassiana s.lat. Some of the genetic groups as previously detected within both taxa were either confirmed or fused using population genomics. High levels of divergence were found between two clades in B. asiatica and among three clades in B. bassiana, supporting their subdivision as distinct species. Morphological examination focusing on the width and the length of phialides and conidia showed no difference among the clades within B. bassiana while conidial length was significantly different among clades within B. asiatica. The secondary metabolite profiles obtained by liquid chromatography-mass spectrometry (LC-MS) allowed a distinction between B. asiatica and B. bassiana, but not between the clades therein. Based on these genomic, morphological, chemical data, we proposed a clade of B. asiatica as a new species, named B. thailandica, and two clades of B. bassiana to respectively represent B. namnaoensis and B. neobassiana spp. nov. Such closely related but divergent species with different host ranges have potential to elucidate the evolution of host specificity, with potential biocontrol application. Citation: Kobmoo N, Arnamnart N, Pootakham W, et al. 2021. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. Persoonia 47: 136-150. https://doi.org/10.3767/persoonia.2021.47.04.

Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships

Bruguiera is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of Bruguiera species are limited. Here, the complete chloroplast sequences of five Bruguiera species were sequenced and assembled using Illumina data. The chloroplast genomes of B. gymnorhiza, B. hainesii, B. cylindrica, B. parviflora and B. sexangula were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, B. gymnorhiza lost a rpl32 gene in the SSC region. In addition, a ndhF gene in B. parviflora straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among Bruguiera species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between B. cylindrica and B. hainesii as well as B. gymnorhiza and B. sexangula indicating close genetic relationships based on maternal inheritance. Notably, B. hainesii, which is considered a hybrid between B. gymnorhiza and B. cylindrica, appears to have inherited the chloroplast from B. cylindrica. Investigating the effects of selection events on shared protein-coding genes showed a positive selection in rps7 and rpl36 genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all Bruguiera species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in Bruguiera and other mangrove species.

The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses

Fungi are rich in complexes of cryptic species that need a combination of different approaches to be delimited, including genomic information. Beauveria (Cordycipitaceae, Hypocreales) is a well-known genus of entomopathogenic fungi, used as a biocontrol agent. In this study we present a polyphasic taxonomy regarding two widely distributed complexes of Beauveria: B. asiatica and B. bassiana s.lat. Some of the genetic groups as previously detected within both taxa were either confirmed or fused using population genomics. High levels of divergence were found between two clades in B. asiatica and among three clades in B. bassiana, supporting their subdivision as distinct species. Morphological examination focusing on the width and the length of phialides and conidia showed no difference among the clades within B. bassiana while conidial length was significantly different among clades within B. asiatica. The secondary metabolite profiles obtained by liquid chromatography-mass spectrometry (LC-MS) allowed a distinction between B. asiatica and B. bassiana, but not between the clades therein. Based on these genomic, morphological, chemical data, we proposed a clade of B. asiatica as a new species, named B. thailandica, and two clades of B. bassiana to respectively represent B. namnaoensis and B. neobassiana spp. nov. Such closely related but divergent species with different host ranges have potential to elucidate the evolution of host specificity, with potential biocontrol application. Citation: Kobmoo N, Arnamnart N, Pootakham W, et al. 2021. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. Persoonia 47: 136-150. https://doi.org/10.3767/persoonia.2021.47.04.

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes

To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.

Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes

Corals live with complex assemblages of microbes including bacteria, the dinoflagellate Symbiodiniaceae, fungi and viruses in a coral holobiont. These coral-associated microorganisms play an important role in their host fitness and survival. Here, we investigated the structure and diversity of algal and bacterial communities associated with five Indo-Pacific coral species, using full-length 16S rRNA and internal transcribed spacer sequences. While the dinoflagellate communities associated with Poriteslutea were dominated with Symbiodiniaceae genus Cladocopium, the other four coral hosts were associated mainly with members of the Durusdinium genus, suggesting that host species was one of the underlying factors influencing the structure and composition of dinoflagellate communities associated with corals in the Gulf of Thailand. Alphaproteobacteria dominated the microbiomes of Pocillopora spp. while Pavonafrondifera and P. lutea were associated primarily with Gammaproteobacteria. Finally, we demonstrated a superior performance of full-length 16S rRNA sequences in achieving species-resolution taxonomic classification of coral-associated microbiota.

De novo chromosome-level assembly of the Centella asiatica genome

Centella asiatica is a herbaceous, perennial species indigenous to India and Southeast Asia. C. asiatica possesses several medicinal properties: anti-aging, anti-inflammatory, wound healing and memory enhancing. The lack of available genomics resources significantly impedes the improvement of C. asiatica varieties through molecular breeding. Here, we combined the 10× Genomics linked-read technology and the long-range HiC technique to obtain the genome assembly. The final assembly contained nine pseudomolecules, corresponding to the haploid chromosome number in C. asiatica. These nine chromosomes covered 402,536,584 bases or 93.6% of the 430-Mb assembly. Comparative genomics analyses based on single-copy orthologous genes showed that C. asiatica and the common ancestor of Coriandrum sativum (coriander) and Daucus carota (carrot) diverged about 48 million years ago. This assembly provides a valuable reference genome for future molecular studies, varietal development through marker-assisted breeding and comparative genomics studies in C. asiatica.

The complete mitochondrial genome sequence of the mountain crab Indochinamon bhumibol

Indochinamon bhumibol has been found as the biggest freshwater crab in Thailand. In this study, we report the first complete sequence of mitochondrial genome from I. bhumibol encoding 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. The nucleotide composition of I. bhumibol mitogenome showed a strong AT bias (70.4%) with a low GC content (29.6%). Comparative phylogenetic analysis with 28 crustaceans based on nine conserved genes demonstrated that I. bhumibol was closely related to members of the Potamidae family.

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.

Assembly of the durian chloroplast genome using long PacBio reads

We have assembled the complete sequence of the Durio zibethinus chloroplast genome using long PacBio reads. Durian is a valuable commercial tree that produces durian fruit, which is popular in Southeast Asia. The chloroplast genome assembled into a single 143 kb cyclic contig that contained 111 genes. There were 46 short direct repeats (45 to 586 bp) and five short inverted repeats (63 to 169 bp). The long reads that were used for the assembly span the entire chloroplast with > 10 kb overlaps and multiple long reads join the start of the contig to the end of the contig. The durian chloroplast was found to lack the large inverted repeat that is common in chloroplast genomes. An additional 24 durian varieties were sequenced and compared to the assembly and found to also lack the large inverted repeat. There were nine SNPs among the varieties.

The Genome and Transcriptome Analysis of the Vigna mungo Chloroplast

Vigna mungo is cultivated in approximately 5 million hectares worldwide. The chloroplast genome of this species has not been previously reported. In this study, we sequenced the genome and transcriptome of the V. mungo chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., rbcL, ndhF, and atpF) and RNA polymerase genes (e.g., rpoC2) from the comparison of the chloroplast genome of V. mungo, temperate legume species, and tropical legume species. Our transcriptome data from PacBio isoform sequencing showed that the 51-kb DNA inversion could affect the transcriptional regulation of accD polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of clpP in the leaf, shoot, flower, fruit, and root tissues of V. mungo. We also found three G-to-A RNA editing events that change guanine to adenine in the transcripts transcribed from the adenine-rich regions of the ycf4 gene. The edited guanine bases were found particularly in the chloroplast genome of the Vigna species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The V. mungo chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering.

A chromosome-scale assembly of the black gram (Vigna mungo) genome

Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked-read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long-range Chicago and HiC techniques yielded the first high-quality, chromosome-level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome-wide duplication event observed in the tetraploid créole bean (Vigna reflexo-pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full-length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high-quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker-assisted breeding and for future comparative genomics and phylogenetic studies in legume species.

De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements

Luffa spp. (sponge gourd or ridge gourd) is an economically important vegetable crop widely cultivated in China, India and Southeast Asia. Here, we employed PacBio long-read single-molecule real-time (SMRT) sequencing to perform de novo genome assemblies of two commonly cultivated Luffa species, L. acutangula and L. cylindrica. We obtained preliminary draft genomes of 734.6 Mb and 689.8 Mb with scaffold N50 of 786,130 and 578,616 bases for L. acutangula and L. cylindrica, respectively. We also applied long-range Chicago and HiC techniques to obtain the first chromosome-scale whole-genome assembly of L. acutangula. The final assembly contained 13 pseudomolecules, corresponding to the haploid chromosome number in Luffa spp. (1n = 13, 2n = 26). The sizes of the assembled Luffa genomes are approximately twice as large as the genome assemblies of related Cucurbitaceae. A large proportion of L. acutangula (62.17%; 456.69 Mb) and L. cylindrica (56.78%; 391.65 Mb) genome assemblies contained repetitive elements. Phylogenetic analyses revealed that the substantial accumulation of transposable elements likely contributed to the expansion of the Luffa genomes. We also investigated alternative splicing events in Luffa using full-length transcript sequences obtained from PacBio Isoform Sequencing (Iso-seq). While the predominant form of alternative splicing in most plant species examined was intron retention, alternative 3' acceptor site selection appeared to be a major event observed in Luffa. High-quality genome assemblies for L. acutangula and L. cylindrica reported here provide valuable resources for Luffa breeding and future genetics and comparative genomics studies in Cucurbitaceae.

Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome

Sugarcane contributes 80% of global sugar production and to bioethanol generation for the bioenergy industry. Its productivity is threatened by drought that can cause up to 60% yield loss. This study used RNA-Seq to gain a better understanding of the underlying mechanism by which drought-tolerant sugarcane copes with water stress. We compared gene expression in KPS01-12 (drought-tolerant genotype) and UT12 (drought-sensitive genotype) that have significantly different yield loss rates under drought conditions. We treated KPS01-12 and UT12 with mild and moderate water stress and found differentially expressed genes in various biological processes. KPS01-12 had higher expression of genes that were involved in water retention, antioxidant secondary metabolite biosynthesis, and oxidative and osmotic stress response than UT12. In contrast, the sensitive genotype had more down-regulated genes that were involved in photosynthesis, carbon fixation and Calvin cycle than the tolerant genotype. Our obtained expression profiles suggest that the tolerant sugarcane has a more effective genetic response than the sensitive genotype at the initiation of drought stress. The knowledge gained from this study may be applied in breeding programs to improve sugarcane production in drought conditions.

The complete mitochondrial genome of Luffa acutangula

Based on PacBio de novo assembly, we report the first complete mitochondrial genome of Luffa acutangula (460,333 bp) containing nine large chloroplast-derived sequences (1.9–17.3 kb) across the mitogenome. The base composition of the mitogenome in descending order is A: 28.02%, C: 22.04%, G: 21.83% and T: 28.10%, and the G + C content is 43.87%. There are 63 mitochondrial genes including 40 protein-coding genes, 3 rRNA genes and 20 tRNA genes. Additionally, a total of 288 repeats ranging from 31 to 5,301 bp were identified, accounting for 5.7% of the mitogenome. Two large direct repeats (5,301 and 405 bp) within the mitogenome were found for the formation of four subgenomic molecules. A phylogenetic analysis showed that L. acutangula was closely related to other species in Cucurbiaceae. This mitogenome provides useful genetic information for evolutionary studies.

Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea

The coral holobiont is a complex ecosystem consisting of coral animals and a highly diverse consortium of associated microorganisms including algae, fungi, and bacteria. Several studies have highlighted the importance of coral‐associated bacteria and their potential roles in promoting the host fitness and survival. Recently, dynamics of coral‐associated microbiomes have been demonstrated to be linked to patterns of coral heat tolerance. Here, we examined the effect of elevated seawater temperature on the structure and diversity of bacterial populations associated with Porites lutea, using full‐length 16S rRNA sequences obtained from Pacific Biosciences circular consensus sequencing. We observed a significant increase in alpha diversity indices and a distinct shift in microbiome composition during thermal stress. There was a marked decline in the apparent relative abundance of Gammaproteobacteria family Endozoicomonadaceae after P. lutea had been exposed to elevated seawater temperature. Concomitantly, the bacterial community structure shifted toward the predominance of Alphaproteobacteria family Rhodobacteraceae. Interestingly, we did not observe an increase in relative abundance of Vibrio‐related sequences in our heat‐stressed samples even though the appearance of Vibrio spp. has often been detected in parallel with the increase in the relative abundance of Rhodobacteraceae during thermal bleaching in other coral species. The ability of full‐length 16S rRNA sequences in resolving taxonomic uncertainty of associated bacteria at a species level enabled us to identify 24 robust indicator bacterial species for thermally stressed corals. It is worth noting that the majority of those indicator species were members of the family Rhodobacteraceae. The comparison of bacterial community structure and diversity between corals in ambient water temperature and thermally stressed corals may provide a better understanding on how bacteria symbionts contribute to the resilience of their coral hosts to ocean warming.

Transcriptome analysis of oil palm inflorescences revealed candidate genes for an auxin signaling pathway involved in parthenocarpy

Oil palm parthenocarpic fruits, which are produced without fertilization, can be targeted to increase oil content because the majority of the fruit is occupied by mesocarp, the part in which palm oil is stored. Consequently, gaining an understanding of the parthenocarpic mechanism would be instrumental for producing parthenocarpic oil palm. This study aims to determine effects of auxin treatment and analyze differentially expressed genes in oil palm pistils at the pollination/anthesis stage, using an RNA sequencing (RNA seq) approach. The auxin treatment caused 100% parthenocarpy when auxin was sprayed before stigmas opened. The parthenocarpy decreased to 55%, 8% and 5% when the auxin was sprayed 1, 2 and 3 days after the opening of stigmas, respectively. Oil palm plants used for RNA seq were plants untreated with auxin as controls and auxin-treated plants on the day before pollination and 1 day after pollination. The number of raw reads ranged from 8,425,859 to 11,811,166 reads, with an average size ranging from 99 to 137 base pairs (bp). When compared with the oil palm transcriptome, the mapped reads ranged from 8,179,948 to 11,320,799 reads, representing 95.85–98.01% of the oil palm matching. Based on five comparisons between RNA seq of treatments and controls, and confirmation using reverse transcription polymerase chain reaction and quantitative real-time RT-PCR expression, five candidate genes, including probable indole-3-acetic acid (IAA)-amido synthetase GH3.8 (EgGH3.8), IAA-amido synthetase GH3.1 (EgGH3.1), IAA induced ARG7 like (EgARG7), tryptophan amino transferase-related protein 3-like (EgTAA3) and flavin-containing monooxygenase 1 (EgFMO1), were differentially expressed between auxin-treated and untreated samples. This evidence suggests a pathway of parthenocarpic fruit development at the beginning of fruit development. However, more research is needed to identify which genes are definitely involved in parthenocarpy.

Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing

Background

Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs.

Methods

We generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors.

Results

A total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants.

Discussion

The new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar.

Genome-wide association mapping of virulence gene in rice blast fungus Magnaporthe oryzae using a genotyping by sequencing approach

Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996-2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. An association study was performed to identify single nucleotide polymorphisms (SNPs) associated with virulence genes using 831 selected SNP and infection phenotypes on local and improved rice varieties. Population structure analysis revealed eight subpopulations. The division into eight groups was not related to the degree of virulence. Association mapping showed five SNPs associated with fungal virulence on chromosome 1, 2, 3, 4 and 7. The SNP on chromosome 1 was associated with virulence against RD6-Pi7 and IRBL7-M which might be linked to the previously reported AvrPi7.

Dynamics of coral-associated microbiomes during a thermal bleaching event

Coral‐associated microorganisms play an important role in their host fitness and survival. A number of studies have demonstrated connections between thermal tolerance in corals and the type/relative abundance of Symbiodinium they harbor. More recently, the shifts in coral‐associated bacterial profiles were also shown to be linked to the patterns of coral heat tolerance. Here, we investigated the dynamics of Porites lutea‐associated bacterial and algal communities throughout a natural bleaching event, using full‐length 16S rRNA and internal transcribed spacer sequences (ITS) obtained from PacBio circular consensus sequencing. We provided evidence of significant changes in the structure and diversity of coral‐associated microbiomes during thermal stress. The balance of the symbiosis shifted from a predominant association between corals and Gammaproteobacteria to a predominance of Alphaproteobacteria and to a lesser extent Betaproteobacteria following the bleaching event. On the contrary, the composition and diversity of Symbiodinium communities remained unaltered throughout the bleaching event. It appears that the switching and/or shuffling of Symbiodinium types may not be the primary mechanism used by P. lutea to cope with increasing seawater temperature. The shifts in the structure and diversity of associated bacterial communities may contribute more to the survival of the coral holobiont under heat stress.

High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.

The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads

Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum and several other Saccharum species. Historical records identify New Guinea as the origin of S. officinarum and that a small number of plants originating from there were used to generate all modern commercial cultivars. The mitochondrial genome can be a useful way to identify the maternal origin of commercial cultivars. We have used the PacBio RSII to sequence and assemble the mitochondrial genome of a South East Asian commercial cultivar, known as Khon Kaen 3. The long read length of this sequencing technology allowed for the mitochondrial genome to be assembled into two distinct circular chromosomes with all repeat sequences spanned by individual reads. Comparison of five commercial hybrids, two S. officinarum and one S. spontaneum to our assembly reveals no structural rearrangements between our assembly, the commercial hybrids and an S. officinarum from New Guinea. The S. spontaneum, from India, and one sample of S. officinarum (unknown origin) are substantially rearranged and have a large number of homozygous variants. This supports the record that S. officinarum plants from New Guinea are the maternal source of all modern commercial hybrids.