Yuxin Yin

The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)

Background Date palm (Phoenix dactylifera L.), a member of Arecaceae family, is one of the three major economically important woody palms—the two other palms being oil palm and coconut tree—and its fruit is a staple food among Middle East and North African nations, as well as many other tropical and subtropical regions. Here we report a complete sequence of the data palm chloroplast (cp) genome based on pyrosequencing. Methodology/Principal Findings After extracting 369,022 cp sequencing reads from our whole-genome-shotgun data, we put together an assembly and validated it with intensive PCR-based verification, coupled with PCR product sequencing. The date palm cp genome is 158,462 bp in length and has a typical quadripartite structure of the large (LSC, 86,198 bp) and small single-copy (SSC, 17,712 bp) regions separated by a pair of inverted repeats (IRs, 27,276 bp). Similar to what has been found among most angiosperms, the date palm cp genome harbors 112 unique genes and 19 duplicated fragments in the IR regions. The junctions between LSC/IRs and SSC/IRs show different features of sequence expansion in evolution. We identified 78 SNPs as major intravarietal polymorphisms within the population of a specific cp genome, most of which were located in genes with vital functions. Based on RNA-sequencing data, we also found 18 polycistronic transcription units and three highly expression-biased genes—atpF, trnA-UGC, and rrn23. Conclusions Unlike most monocots, date palm has a typical cp genome similar to that of tobacco—with little rearrangement and gene loss or gain. High-throughput sequencing technology facilitates the identification of intravarietal variations in cp genomes among different cultivars. Moreover, transcriptomic analysis of cp genes provides clues for uncovering regulatory mechanisms of transcription and translation in chloroplasts.

Genome sequence of the date palm Phoenix dactylifera L

Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (~671 Mb) and >96% of its genes (~41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm’s unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.

A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome.

Based on next-generation sequencing data, we assembled the mitochondrial (mt) genome of date palm (Phoenix dactylifera L.) into a circular molecule of 715,001 bp in length. The mt genome of P. dactylifera encodes 38 proteins, 30 tRNAs, and 3 ribosomal RNAs, which constitute a gene content of 6.5% (46,770 bp) over the full length. The rest, 93.5% of the genome sequence, is comprised of cp (chloroplast)-derived (10.3% with respect to the whole genome length) and non-coding sequences. In the non-coding regions, there are 0.33% tandem and 2.3% long repeats. Our transcriptomic data from eight tissues (root, seed, bud, fruit, green leaf, yellow leaf, female flower, and male flower) showed higher gene expression levels in male flower, root, bud, and female flower, as compared to four other tissues. We identified 120 potential SNPs among three date palm cultivars (Khalas, Fahal, and Sukry), and successfully found seven SNPs in the coding sequences. A phylogenetic analysis, based on 22 conserved genes of 15 representative plant mitochondria, showed that P. dactylifera positions at the root of all sequenced monocot mt genomes. In addition, consistent with previous discoveries, there are three co-transcribed gene clusters–18S-5S rRNA, rps3-rpl16 and nad3-rps12–in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms.

Chasing relationships between nutrition and reproduction: A comparative transcriptome analysis of hepatopancreas and testis from Eriocheir sinensis.

There is a delicate relationship between nutrition and reproduction of mitten crab (Eriocheir sinensis). The crabs store significant amounts of energy in hepatopancreas, which is prepared for significant energy output and expenditure during reproduction, but the internal molecular mechanism has never been known. Here we present the first relationship between hepatopancreas and testis of E. sinensis. We acquired 6287 high quality expressed sequence tags (EST), representing 3829 unigenes totally, from healthy male mitten crabs of first grade. We investigated the Gene Ontology and the main metabolism processes of hepatopancreas and testis from E. sinensis. Genes most likely expressed more frequently and localized in hepatopancreas, and abundant genes from testis for multiple functions. Many genes important for the nutrition regulation are in the EST resource, including arginine kinase, leptin receptor-like protein, seminal plasma glycoprotein 120, and many kinds of zinc finger proteins. The EST data also revealed genes such as heat shock protein 70, testis enhanced gene transcript (TEGT), Cyclin K, etc. predicted to play important roles in regulation of reproduction mechanisms. Among these genes, alignment of leptin receptor-like protein and vasa-like protein from E. sinensis and other species showed even more genomic information on E. sinensis. We identified seventeen genes relevant to control of nutrition mechanisms and eleven genes involved in regulation of reproduction. And this study provides insights into the genetic and molecular mechanisms of nutrition and reproduction in the crab. Such information would facilitate the optimization of breeding in the aquaculture of mitten crabs.

Identification of Genes Involved in Immune Response, Microsatellite, and SNP Markers from Expressed Sequence Tags Generated from Hemocytes of Freshwater Pearl Mussel (Hyriopsis cumingii)

Triangle sail mussel (Hyriopsis cumingii) is the most important mussel species commercially exploited for freshwater pearl production in China. However, its genome research is still at the infantry. Genomic resources for this species are largely not available. The objectives of this study was to generate expressed sequence tags from a hemocyte cDNA library, to identify genes involved in defense mechanisms, and to identify polymorphic markers from the expressed sequence tag (EST) resources for genetic analysis. A total of 5,290 ESTs were sequenced, obtaining 481 contigs and 1,165 singletons. BLAST similarity analysis indicated almost half (46.5%) of these ESTs were homologs of known genes while 53.5% were transcripts of unknown identities. Based on sequence similarities, 50 genes were identified as putative genes involved in immune and defense functions such as hemocyte immune process, stress proteins, adhesive proteins, proteases and protease regulators, antimicrobial peptides, lysosomal enzymes, cell apoptosis, and cell cycle proteins. A total of 201 microsatellites were identified from these ESTs, with 31 having sufficient flanking sequences for primer design. Polymerase chain reaction amplification was successful for 18 primer pairs and 14 of them were polymorphic. A total of 987 putative single nucleotide polymorphisms were identified including 204 transitions, 611 transversions, and 172 indels; 12 of them were involved in nine genes of defense mechanisms. These resources provide the material basis for future marker validation and genetic linkage and quantitative trait loci analysis in the freshwater pearl mussel.

Whole genome sequencing of lamb rotavirus and comparative analysis with other mammalian rotaviruses

Rotavirus (RV) epidemiological surveys with molecular analysis of various strains are required for gastroenteritis control and prevention. The lamb rotavirus strain NT, isolated from a diarrhea lamb in China, is considered as a promising vaccine strain. The whole genome of the lamb-NT strain was determined by sequence analysis. Sequence identity and phylogenetic analysis defined the lamb-NT strain as group A, genotype G10P[15]/NSP4[A]/SG1 strain. Comparative genomic analysis of the lamb-NT strain and 17 reference strains reveals that gene reassortments between rotaviruses circulating in different species occurred. Alignment of protein sequences of the genes shows some variations in the important functional regions of VP3 and VP4. These variations are related to host range restriction, virulence, and other potential characters of rotaviruses. Besides, this study also makes a significant foundation for the study of genetic classification, epidemiology, and antigenic diversity of rotaviruses on the molecular level.

Identification of Genes Potentially Involved in Pearl Formation by Expressed Sequence Tag Analysis of Mantle from Freshwater Pearl Mussel (Hyriopsis Cumingii Lea)

ABSTRACT The triangle sail mussel (Hyriopsis cumingii Lea) is the most important mussel species exploited for commercial freshwater pearl production in China. However, little is known about the genes that arc involved in pearl formation. A complementary DNA library from mantle tissue of Hyriopsis cumingii was constructed to identify the genes required for pearl formation. A total of 5,019 expressed sequence tags (ESTs) were sequenced, which resulted in the identification of 620 contigs and 1,151 singletons. BLAST analysis showed that nearly half (44.7%) of these unigenes were homologous to the known genes and 55.3% were genes with unknown functions. Based on the sequence similarities, 29 genes were putatively involved in pearl formation. These EST data provide the basis for future studies of the molecular mechanisms underlying pearl formation.

A large-scale gene discovery for the red palm weevil Rhynchophorus ferrugineus （Coleoptera： Curculionidae）

The red palm weevil (RPW; Rhynchophorus ferrugineus) is a devastating pest of palms, prevalent in the Middle East as well as many other regions of the world. Here, we report a large‐scale de novo complementary DNA (cDNA) sequencing effort that acquired ∼5 million reads and assembled them into 26 765 contigs from 12 libraries made from samples of different RPW developmental stages based on the Roche/454 GS FLX platform. We annotated these contigs based on the publically available known insect genes and the Tribolium castaneum genome assembly. We find that over 80% of coding sequences (CDS) from the RPW contigs have high‐identity homologs to known proteins with complete CDS. Gene expression analysis shows that the pupa and larval stages have the highest and lowest expression levels, respectively. In addition, we also identified more than 60 000 single nucleotide polymorphisms and 1 200 simple sequence repeat markers. This study provides the first large‐scale cDNA dataset for RPW, a much‐needed resource for future molecular studies.

Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is an invasive, concealed and destructive tissue borer, and it becomes a lethal pest of the palm family of plants and has been reported to attack 20 palm species around the globe. Here we report a systematic transcriptomic study on embryogenesis of RPW, where we analyze the transcriptomes across five developmental stages of RPW embryogenesis, involving four embryonic stages (E1, E2, E3 and E4) and one larval stage (L1). Using the RNA‐seq and next‐generation platforms, we generated 80 to 91 million reads for each library and assemble 22 532 genes that are expressed at different embryonic stages. Among the total transcripts from the five embryonic development stages, we found that 30.45 % are differentially expressed, 10.10 % show stage‐specificity and even a larger fraction, 62.88 %, exhibit constitutive expression in all the stages. We also analyzes the expression dynamics of several conserved signaling pathways (such as Hedgehog, JAK‐STAT, Notch, TGF‐β, Ras/MAPK and Wnt), as well as key developmental genes, including those related to apoptosis, axis formation, Hox complex, neurogenesis and segmentation. The datasets provide an essential resource for gene annotation and RPW functional genomics, including studies by using tools and concepts from multiple disciplines, such as development, physiology, biochemistry, molecular biology and genetics.

Date Palm Genome Project at the Kingdom of Saudi Arabia

The Date Palm Genome Project of the Kingdom of Saudi Arabia is a comprehensive genome research project aimed at sequencing the date palm genome to completion, deciphering the transcriptomes and understanding the biology of date palm for improved cultivation and pest prevention. We introduce plant genomics and its technological advancement, tools and resources used for plant genomics and the scope, goals and recent progress of the Project. Up to date, we generated about 30 M 454 reads (∼15× coverage) and have assembly it into 226,501 contigs, with a total length of 416,498,895 bps. In addition, we achieved the whole 158,462 bp double-stranded circular plastid genome, which with a typical quadripartite structure of the large (LSC, 86,198 bp) and small single copy (SSC, 17,712 bp) regions separated by a pair of inverted repeats (IRs, 27,276 bp). Moreover, in excess of 5,000,000 date palm cDNAs have been sequenced by a 454 sequencer, and these EST sequences will play an important role for date palm genome assembly and gene annotation. In future, more than 100× coverage of SOLiD long mate pair reads will be used to increase the quality of genome assembly, and used to construct scaffolds. Further analysis of date palm genome will be performed in the coming months.