news and views End of the beginning Lincoln D. Stein Just over three years ago, it was announced that a first draft of the human genome sequence had been completed. Gaps and errors remained, but the job of fixing those problems is now largely done T issue of nature features mutation that rendered the gene non-g n article entitled"Finishin functional. The resulting pseudogene then slowly degrades and disappears. the human genome. It has been 上了 In a second analysis, the authors authored by members of the Inter use the finished sequence to map national Human Genome Sequen out segmental duplications- large Consortium (IHGSC), and f the genome that have appears on page 931. The article ey marks the latest, but by no means 5% of the genome is the last, milestone in this historic involved in segmental duplications, project. But readers can be forgiven and that the distribution of these for being a bit confused by the regions varies widely across the announcement. Wasn't the human chromosomes. Knowing the nature genome finished several years ago? and extent of such duplications is The answer is yes'-and ne important for understanding the Early in 2001, the duelling IHGSC olution of the human genom (public) and Celera Corporation d for studying the many medically (private) groups published papers elevant disorders that are involved in Nature- and Science'describing n segmental duplications, such as the completion of so-called draft DiGeorge syndrome and Charcot- sequences. These sequences have Marie-Tooth syndrome. revolutionized molecular biology Another paper in this issue, by She by largely eliminating the need et al. (page 927), directly compares clone and sequence genes involved in the outcomes of this second analysis human health and disease. Instead of with results obtained on an unfin- going to the bench, biologists now go ished version of the human genome the web to look up gene sequences (an improved version of the Celera in public online databases draft). She et al. find that the draft But despite their immediate use- version artefactually simplifiesthe fulness, the draft sequences were fa genome by eliminating many dupli- from perfect. Both drafts were miss- ted regions. Their results bear on ing some 10% of the so-called one of the highly publicized differ euchromatin'-the gene-rich por- ences between the public and private tion of the genome-and some 30% of the of DNA. The sequence announced today genome projects. The public project used ar genome as a whole(which includes the gene- has just 341 gaps remaining, and consists older strategy in which the genomomosomes poor regions of heterochromatin ). The of contiguous runs of sequence averaging cloned into bacterial artificia men a their drafts contained hundreds of thousands of 38 million base pairs. The authors estimate (BACs); the clones were gaps, and had misassembled regions where that the finished sequence covers 99% of the and each clone was rtions of the genome were flipped or mis- euchromatic portion of the genome and that sequences assembled individually. Celera placed As aresult, any large-scale analyses of the overall error rate is less than I error per championed an untested technique, whole the genome, such as studies of the mecha- 100,000 base pairs. This substantially exceeds genome shotgun(WGS), in which the entire nisms of gene evolution or the long-range the original goals for the project. genome was shattered into bite-size pieces, structure of the genome, had to contend with The finishing procedure roughly doubled sequenced, and then assembled by software example, studies of pseudogenes, the dying contribute anything new to our understand. In one conceptually simple step Celera proved that the WGS technique remnants of genes that have accumulated ing of the genome? It does indeed, and to is both technically feasible and provides mutations thatrender them non-functional, prove the point the authors of the current a dramatic cost-saving over the clone-by had to contend with the possibility that any paper describe several large-scale analyses clone approach. Although the Celera draft apparent pseudogene was instead the result of the genome that would have been difficult has languished because the availability of sequencing error. perform on the draft sequence. Oneanaly- public data in free online databases under Since the publication of the drafts, sis studied the processes of gene birth and mined the company's business plan to sell the IHGSC sequencing centres have quietly death. The authors find 1, 183 human genes genome-database subscriptions, the effort undertaken alaborious'finishing' process, in that show evidence of having been recently left a permanent mark on the public project. which each gap in the draft was individually born by a process of gene duplication and Almost all genome-sequencing projects examined and subjected to a battery of steps divergence. They also find 37 genes that since then have used some form of wGS volvingcloning and resequencing stretches seem to have recently died by acquiring a The cautionary results contained in the new NatuRevOl43121OctOber2004www.nature.com/nature 915 @2004 Nature Publishing Group
This issue of Nature features an article1 entitled “Finishing the euchromatic sequence of the human genome”. It has been authored by members of the International Human Genome Sequencing Consortium (IHGSC), and appears on page 931. The article marks the latest, but by no means the last, milestone in this historic project. But readers can be forgiven for being a bit confused by the announcement. Wasn’t the human genome ‘finished’ several years ago? The answer is ‘yes’ — and ‘no’. Early in 2001, the duelling IHGSC (public) and Celera Corporation (private) groups published papers in Nature 2 and Science 3 describing the completion of so-called ‘draft’ sequences. These sequences have revolutionized molecular biology by largely eliminating the need to clone and sequence genes involved in human health and disease. Instead of going to the bench, biologists now go to the web to look up gene sequences in public online databases. But despite their immediate usefulness, the draft sequences were far from perfect. Both drafts were missing some 10% of the so-called ‘euchromatin’ — the gene-rich portion of the genome — and some 30% of the genome as a whole (which includes the genepoor regions of ‘heterochromatin’). The drafts contained hundreds of thousands of gaps, and had misassembled regions where portions of the genome were flipped or misplaced.As a result, any large-scale analyses of the genome, such as studies of the mechanisms of gene evolution or the long-range structure of the genome,had to contend with numerous uncertainties and artefacts. For example, studies of ‘pseudogenes’, the dying remnants of genes that have accumulated mutations that render them non-functional, had to contend with the possibility that any apparent pseudogene was instead the result of a sequencing error. Since the publication of the drafts, the IHGSC sequencing centres have quietly undertaken a laborious ‘finishing’process,in which each gap in the draft was individually examined and subjected to a battery of steps involving cloning and resequencing stretches of DNA. The sequence announced today has just 341 gaps remaining, and consists of contiguous runs of sequence averaging 38 million base pairs. The authors estimate that the finished sequence covers 99% of the euchromatic portion of the genome and that the overall error rate is less than 1 error per 100,000 base pairs. This substantially exceeds the original goals for the project. The finishing procedure roughly doubled the total time and cost of the project. Does it contribute anything new to our understanding of the genome? It does indeed, and to prove the point the authors of the current paper1 describe several large-scale analyses of the genome that would have been difficult toperform on the draft sequence.One analysis studied the processes of gene birth and death. The authors find 1,183 human genes that show evidence of having been recently ‘born’ by a process of gene duplication and divergence. They also find 37 genes that seem to have recently ‘died’ by acquiring a news and views NATURE|VOL 431 | 21 OCTOBER 2004 |www.nature.com/nature 915 mutation that rendered the gene nonfunctional. The resulting pseudogene then slowly degrades and disappears. In a second analysis, the authors use the finished sequence to map out segmental duplications — large regions of the genome that have duplicated in recent evolution. They find that 5% of the genome is involved in segmental duplications, and that the distribution of these regions varies widely across the chromosomes. Knowing the nature and extent of such duplications is important for understanding the evolution of the human genome, and for studying the many medically relevant disorders that are involved in segmental duplications, such as DiGeorge syndrome and Charcot– Marie–Tooth syndrome. Another paper in this issue,by She et al.4 (page 927), directly compares the outcomes of this second analysis with results obtained on an unfinished version of the human genome (an improved version of the Celera draft). She et al. find that the draft version artefactually ‘simplifies’ the genome by eliminating many duplicated regions. Their results bear on one of the highly publicized differences between the public and private genome projects. The public project used an older strategy in which the genome was first cloned into bacterial artificial chromosomes (BACs); the clones were then mapped, and each clone was sequenced and their sequences assembled individually. Celera championed an untested technique, ‘wholegenome shotgun’(WGS), in which the entire genome was shattered into bite-size pieces, sequenced, and then assembled by software in one conceptually simple step. Celera proved that the WGS technique is both technically feasible and provides a dramatic cost-saving over the clone-byclone approach. Although the Celera draft has languished because the availability of public data in free online databases undermined the company’s business plan to sell genome-database subscriptions, the effort left a permanent mark on the public project. Almost all genome-sequencing projects since then have used some form of WGS. The cautionary results contained in the new End of the beginning Lincoln D. Stein Just over three years ago, it was announced that a first draft of the human genome sequence had been completed. Gaps and errors remained, but the job of fixing those problems is now largely done. GETTY IMAGES 21.10 n&v 915 MH 15/10/04 5:34 pm Page 915 © 2004 NaturePublishingGroup
news and views papers from the IHGSC and She et al. Much farther in the future is the task of split into two distinct evolutionary lineages argue for a hybrid strategy in which WGS is sequencing the remaining 20% of thethe actinopterygians (ray-finned fish) supplemented by a modest amount of BAC genome that lies within heterochromatin, which include teleosts suchaspufferfish and draft WGS sequences from some of the that is implicated in the processes of chro- fins), which include lungfish, coelacanths simplification reported by She et al. and mosome replication and maintenance. The and ourselves(Fig. 1). By matching up the provide the clones needed for finishing repetitiveness of heterochromatin means genes on each pufferfish chromosome to the selected regions of special interest that it cannot be tackled using current related genes on human chromosomes, Jail What is next for the human genome pro- sequencing methods, and new technologies lon et al. deduce that the extinct ancestor had ject? Even with a finished sequence in hand will have to be developed to attackit. So dont 12 pairs of chromosomes. Work on partially there is much still to do. Surprisingly, one be shocked to see another paper announcing completed genome sequences had suggested task is to develop the definitive catalogue of the finishing'of the human genome in 2010 this number, but the new analyses add fas- limitations to state-of-the-art gene-predic- researchers ave already climbed mountains animal having been exin es werea e protein-coding genes In the current paper, -it will describe how the heterochromatin cinating detail to the picture. For example, the number is estimated to be between problem has been cracked. s now possible to say which gene 20,000 and 25,000. This wide range reflects In sequencing the human genome, which chromosomes, despite more than tion software that leave doubts about the and travelled a long and winding road. But we 400 million years. validity of many predicted genes. One are at theend of the beginning: aheadlies One puzzling observation concerns the promising approach is to use comparative another mountain range that we will need to apparent stability of the genomes of ray- genomics to align the human genome with map outandexplore as we seek to understand finned fish. It seems that the ancestral the genomes of other animals. Because how all the parts revealed by the genome genome underwent as few as ten large inter- natural selection ensures that functional sequence work together to make life chromosomal rearrangements(exchanges, regions are more highly conserved than Lincoln D. Stein is at Cold Spring Harbor fissionsor fusions) to giverise to the present non-functional ones, this approach high- Laboratory, I Bungtown Road, day Tetraodon genome. Indeed, 11 Tetraodon lights candidate protein-coding regions. The Cold Spring Harbor, New York 11724, USA. same approach shows promise for finding e-mail: Istein@cshLedu such rearrangements. Only one human other functional elements such as gene pro-1Inte Human Genome Sequencing Consortium Nature chromosome(14)can make the same claim, moters, which control the timing and level of 431,931-945(2004). despite the timescale being id expression of genes, and micro-RNAs, which 2. International Human Genome Sequencing Consortium Nature Although the genomes of ray-finned fish have been implicated as regulatory agents of 3. Venter, L.C. et al Science 291, 1304-1351(2001). may have been slowly evolving in terms of many developmental processes. chromosome breakages and fusions, they have experienced a cataclysmic event in their history. Jaillon and colleagues' analyses of the Comparative genomics complete Tetraodon genome sequence show 鲁垂看 clearly that a duplication of the whole Small genome, big insights genome occurred sometime within the ray finned-fish lineage. This inference is not ohn Mulley and Peter Holland new, having been previously suggested from The genome of a second pufferfish species has been sequenced. Why gene families in zebrafish, Takifuguand other is this important? Because comparing this genome with that of other teleosts"-, but the conclusion has remained animals yields a wealth of information on genome evolution controversial Two new analyses should now settle the is still early days for the field of com- two species share a feature of great conve- issue, however. First, Jaillon and collea parative genomics. Only around a dozen nience for genomics: their cells possess less plotted the chromosome positions for al species of animal have so far had their DNA than those of any other group of back- 750 pairs of ancient'duplicated genes within complete DNA sequence determined, even boned animals -about eight or nine times the Tetraodon genome, revealing related to draft coverage. These are predominantly less than human cells. pairs of chromosomes or chromosomal the widely studied model species, such as Although the Tetraodon genome is small regions. Every chromosome is involved, mice, fruitflies and nematode worms, or compared with that of other vertebrates, consistent with an ancient whole-genome species of particularinterest to humans, such sequene as the malaria-carrying mosquito task. Th, g it was still a hugely formidable duplication. In the second test, chromosome research reported in this issue was positions for more than 6,000 pufferfish It may come as a surprise, therefore, to performed in a collaboration between Geno- genes were compared with the positions find that the list now includes not one, but scope in France and the Broad Institute of of related genes in the human genome two species of Tetraodontiformes, a relatively the Massachusetts Institute of Technology This revealed a striking pattern of double obscure group of fish also known as puffers. and Harvard University in the United States. conserved synteny, meaning that one Following on from the publication two Together they have generated a genome chromosomal region in humans matches years ago of the genome sequence of sequence of impressive accuracy and cover- two in pufferfish, across the entire genome. the Japanese pufferfish Takifugu rubi age,with 64% of the DNA sequence mapped This is a clear echo of whole-genome dupli illon and colleagues" report, on page 946 to specific chromosomes ation in the ray-finned-fish lineage Every of this issue, the near-complete sequence By comparing the Tetraodon genome gene, on every chromosome, was duplicated, of the spotted green pufferfish Tetraodon sequence with that of humans, Jaillon et al. although there has since been a massive nigroviridis. Takifugu is a poisonous marine even allow us to peer into the genome of degree of gene loss and local gene shuffling fish best known to connoisseurs of sushi the last common ancestor of pufferfish and When did this whole-genome duplica restaurants, whereas Tetraodon is a small, humans-a primitive bony fish that lived tion occur? Analysis of zebrafish genetic brackish-water pufferfish commonly kept in hundreds of millions of years ago. The maps strongly suggests that this species also aquaria. But, like all Tetraodontiformes, the descendants of this long-extinct ancestor underwent such an event in its history 916 NatuRevoL43121ocTober2004wwW.nature.com/naturE @2004 Nature Publishing Group
two species share a feature of great convenience for genomics: their cells possess less DNA than those of any other group of backboned animals — about eight or nine times less than human cells. Although the Tetraodon genome is small compared with that of other vertebrates, sequencing it was still a hugely formidable task. The research reported in this issue2 was performed in a collaboration between Genoscope in France and the Broad Institute of the Massachusetts Institute of Technology and Harvard University in the United States. Together they have generated a genome sequence of impressive accuracy and coverage, with 64% of the DNA sequence mapped to specific chromosomes3 . By comparing the Tetraodon genome sequence with that of humans, Jaillon et al. even allow us to peer into the genome of the last common ancestor of pufferfish and humans — a primitive bony fish that lived hundreds of millions of years ago. The descendants of this long-extinct ancestor split into two distinct evolutionary lineages: the actinopterygians (ray-finned fish), which include teleosts such as pufferfish and zebrafish, and the sarcopterygians (lobefins), which include lungfish, coelacanths and ourselves (Fig. 1). By matching up the genes on each pufferfish chromosome to the related genes on human chromosomes, Jaillon et al. deduce that the extinct ancestor had 12 pairs of chromosomes. Work on partially completed genome sequences had suggested this number4,5, but the new analyses add fascinating detail to the picture. For example, it is now possible to say which genes were on which chromosomes, despite this unknown animal having been extinct for more than 400 million years. One puzzling observation concerns the apparent stability of the genomes of rayfinned fish. It seems that the ancestral genome underwent as few as ten large interchromosomal rearrangements (exchanges, fissions or fusions) to give rise to the presentday Tetraodon genome.Indeed,11 Tetraodon chromosomes have not experienced any such rearrangements. Only one human chromosome (14) can make the same claim, despite the timescale being identical. Although the genomes of ray-finned fish may have been slowly evolving in terms of chromosome breakages and fusions, they have experienced a cataclysmic event in their history.Jaillon and colleagues’analyses of the complete Tetraodon genome sequence show clearly that a duplication of the whole genome occurred sometime within the rayfinned-fish lineage. This inference is not new, having been previously suggested from analyses of the Hox-gene clusters and other gene families in zebrafish,Takifuguand other teleosts4–7, but the conclusion has remained controversial8 . Two new analyses should now settle the issue, however. First, Jaillon and colleagues plotted the chromosome positions for about 750 pairs of‘ancient’duplicated genes within the Tetraodon genome, revealing related pairs of chromosomes or chromosomal regions. Every chromosome is involved, consistent with an ancient whole-genome duplication. In the second test, chromosome positions for more than 6,000 pufferfish genes were compared with the positions of related genes in the human genome. This revealed a striking pattern of ‘double conserved synteny’, meaning that one chromosomal region in humans matches two in pufferfish, across the entire genome. This is a clear echo of whole-genome duplication in the ray-finned-fish lineage. Every gene,on every chromosome,was duplicated, although there has since been a massive degree of gene loss and local gene shuffling. When did this whole-genome duplication occur? Analysis of zebrafish genetic maps strongly suggests that this species also underwent such an event in its history4 . news and views 916 NATURE|VOL 431 | 21 OCTOBER 2004 |www.nature.com/nature papers from the IHGSC1 and She et al.4 argue for a hybrid strategy in which WGS is supplemented by a modest amount of BAC cloning and mapping. This would protect draft WGS sequences from some of the ‘simplification’ reported by She et al. and provide the clones needed for finishing selected regions of special interest. What is next for the human genome project? Even with a finished sequence in hand there is much still to do. Surprisingly, one task is to develop the definitive catalogue of protein-coding genes. In the current paper1 , the number is estimated to be between 20,000 and 25,000. This wide range reflects limitations to state-of-the-art gene-prediction software that leave doubts about the validity of many predicted genes. One promising approach is to use comparative genomics to align the human genome with the genomes of other animals. Because natural selection ensures that functional regions are more highly conserved than non-functional ones, this approach highlights candidate protein-coding regions.The same approach shows promise for finding other functional elements such as gene promoters,which control the timing and level of expression of genes,and micro-RNAs,which have been implicated as regulatory agents of many developmental processes. Much farther in the future is the task of sequencing the remaining 20% of the genome that lies within heterochromatin, the gene-poor, highly repetitive sequence that is implicated in the processes of chromosome replication and maintenance. The repetitiveness of heterochromatin means that it cannot be tackled using current sequencing methods, and new technologies willhave to be developed to attack it.So don’t be shocked to see another paper announcing the ‘finishing’ of the human genome in 2010 — it will describe how the heterochromatin problem has been cracked. In sequencing the human genome, researchers have already climbed mountains and travelled a long and winding road.But we are only at the end of the beginning:ahead lies another mountain range that we will need to map out and explore as we seek to understand how all the parts revealed by the genome sequence work together to make life. ■ Lincoln D. Stein is at Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA. e-mail: lstein@cshl.edu 1. International Human Genome Sequencing Consortium Nature 431, 931–945 (2004). 2. International Human Genome Sequencing Consortium Nature 409, 860–921 (2001). 3. Venter, J. C. et al. Science 291, 1304–1351 (2001). 4. She, X. et al. Nature 431, 927–930 (2004). I t is still early days for the field of comparative genomics. Only around a dozen species of animal have so far had their complete DNA sequence determined, even to draft coverage. These are predominantly the widely studied model species, such as mice, fruitflies and nematode worms, or species of particular interest to humans,such as the malaria-carrying mosquito. It may come as a surprise, therefore, to find that the list now includes not one, but two species of Tetraodontiformes,a relatively obscure group of fish also known as puffers. Following on from the publication two years ago of the genome sequence of the Japanese pufferfish Takifugu rubripes1 , Jaillon and colleagues2 report, on page 946 of this issue, the near-complete sequence of the spotted green pufferfish Tetraodon nigroviridis. Takifugu is a poisonous marine fish best known to connoisseurs of sushi restaurants, whereas Tetraodon is a small, brackish-water pufferfish commonly kept in aquaria. But, like all Tetraodontiformes, the Comparative genomics Small genome, big insights John Mulley and Peter Holland The genome of a second pufferfish species has been sequenced. Why is this important? Because comparing this genome with that of other animals yields a wealth of information on genome evolution. 21.10 n&v 915 MH 15/10/04 5:34 pm Page 916 © 2004 NaturePublishingGroup